Nucleic acid encoding proteins involved in protein degradation, products and methods related thereof

ABSTRACT

In accordance with the present invention, there are provided novel Siah-Mediated-Degradation-Proteins (SMDPs) and/or SCF-Complex Proteins (SCPs). Nucleic acid sequences encoding such proteins and assays employing same are also disclosed. The invention SMDPs and/or SCPs can be employed in a variety of ways, for example, for the production of anti-SMDP and/or SCP antibodies thereto, in therapeutic compositions, and methods employing such proteins and/or antibodies for drug screening, functional genomics and other applications. Also provided are transgenic non-human mammals that express the invention protein. Also provided are compositions and methods for targeting the destruction of selected polypeptides in eukaryotic cells based on the ubiquitin-independent mechanism by which ornithine decarboxylase is degraded by the 26S proteasome.

This application is a continuation-in-part of application Ser. No. 10/679,246, filed Oct. 2, 2003, which is a continuation-in-part of application Ser. No. 09/591,694, filed Jun. 9, 2000, now U.S. Pat. No. 6,638,734, which claims the benefit of U.S. Provisional Application No. 60/367,334, filed Jun. 11, 1999, which was converted from U.S. Ser. No. 09/330,517, and is incorporated herein by reference.

Portions of the invention described herein were made in the course of research supported in part by grant no. CA69381 from the National Academy of Sciences from the National Institutes of Health. The Government may have certain rights in this invention.

FIELD OF THE INVENTION

The present invention relates to nucleic acids and proteins encoded thereby.

BACKGROUND OF THE INVENTION

The temporal coordination of sequential steps within the eukaryotic cell cycle is governed in large part by protein degradation, involving targeted ubiquitination of specific cell cycle regulatory proteins followed by their destruction by the 26S proteasome (reviewed in Ciechanover, A. 1998, EMBO J., 17(24):7151-7160). Among the cell cycle regulators whose levels are controlled by ubiquitination and subsequent proteosome-dependent degradation are the cyclins (cyclins A, B, C, D1, E) and several of the cyclin-dependent kinase (cdk) inhibitory proteins including p21-Waf1 and p27 Kip. Defects in this highly regulated process of protein turnover have been documented in many types of cancer.

The steps involved in polyubiquitination of specific proteins in cells involve the concerted actions of E1, E2, and E3-type enzymes. E1 proteins form thioester bonds in which the sulfhydryl group of internal cysteine residues binds the carboxyl amino acid of ubiquitin, thereby activating ubiquitin for subsequent transfer to E2-family proteins. E2 family proteins then transfer activated ubiquitin to the free amino-groups of lysine side chains in target proteins directly. More often, however, E2-family proteins collaborate with E3 proteins which bind particular target proteins and orchestrate their interactions with E2s, coordinating the polyubiquitination of these target proteins in highly regulated manners (Ciechanover, 1998, supra). E3 functions are sometimes embodied in multiprotein complexes rather than mediated by a single protein.

The ubiquitination and degradation of a variety of cyclins, cyclin-dependent kinases (cdks) and cdk-inhibitors is temporally controlled during the cell cycle by SFC complexes. Theses multiprotein complexes function as E3-like entities, and contain the Skp-1 protein, at least one Cullin-family protein, and at least one F-box protein, thus the acronym SCF: S=Skp1; C=Cullin; F=F-box) (reviewed in Patton, E. E. et al., 1998, TIG 14(6):236-243). F-box proteins contain a conserved motif, the F-box, which mediates their interactions with Skp-1. The F-box proteins also contain other domains which allow them to simultaneously bind specific substrate proteins, which are then targeted for degradation via polyubiquitination. One such F-box protein identified in humans is b-Trcp, which forms a SCF complex with Skp-1 and Cul-1, and which interacts with β-catenin, targeting it for degradation (Latres, et al., 1999, Oncogene, 18:849-854, and Winston, J. J. et al., 1999, Genes & Dev., 13:270-283).

Siah-family proteins represent mammalian homologs of the Drosophila Sina protein. Sina is required for R7 photoreceptor cell differentiation within the sevenless pathway. Sina binds a ubiquitin-conjugating enzyme (E2) via an N-terminal RING domain. Heterocomplexes of Sina and another protein called Phyllopodia form a E3-complex which interacts with a transcriptional repressor called Tramtrack, targeting it for polyubiqitination and proteosome-mediated degradation in the fly (Tang, A. H. et al., 1997, Cell, 90:459-467 and Li, S. et al., 1997, Cell, 469-478). The destruction of Tramtrack is necessary for differentiation of R7 cells.

At present, little is known about the expression of mammalian genes related to the Siah-mediated-protein-degradation family of proteins in normal cells and cancers. Moreover, the diversity of functions of the Siah-mediated-protein-degradation family proteins remain unclear. Therefore, there continues to be a need in the art for the discovery of additional proteins that interact with the Siah-mediated-protein-degradation pathway, such as proteins that bind Siah in vivo, and especially a need for information serving to specifically identify and characterize such proteins in terms of their amino acid sequence. Moreover, to the extent that such molecules might form the basis for the development of therapeutic and diagnostic agents, it is essential that the DNA encoding them be elucidated. Similarly, a need exists to identify additional components of SCF complexes which may operate in concert with or independently of Siah.

A naturally occurring alternative pathway for proteasome-dependent polypeptide degradation has been identified in ornithine decarboxylase (ODC) and antizyme (AZ) (reviewed in Coffino, Nat. Rev. Mol. Cell Biol. 2:188-194, 2001). ODC directly binds to and is degraded by the 26S proteasome through a mechanism that is catalyzed by AZ and is independent of ubiquitin (Murakami et al., Nature 360:597-599, 1992).

BRIEF DESCRIPTION OF THE INVENTION

In accordance with the present invention, there are provided novel isolated nucleic acids encoding a variety of Siah-Mediated-Degradation-Proteins (SMDPs) involved in the Siah-mediated protein degradation pathways and/or SCF-Complex-Proteins (SCPs) involved in SCF-mediated protein degradation pathways. Further provided are vectors containing invention nucleic acids, probes that hybridize thereto, host cells transformed therewith, antisense-nucleic acids thereto and related compositions. The nucleic acid molecules described herein can be incorporated into a variety of expression systems known to those of skill in the art. In addition, the nucleic acid molecules of the present invention are useful as probes for assaying for the presence and/or amount of a SMDP and/or SCP gene or mRNA transcript in a given sample. The nucleic acid molecules described herein, and oligonucleotide fragments thereof, are also useful as primers and/or templates in a PCR reaction for amplifying genes encoding SMDP and/or SCP proteins.

In accordance with the present invention, there are also provided isolated mammalian SMDP and/or SCP proteins. These proteins, or fragments thereof, are useful in bioassays, as immunogens for producing anti-SMDP and/or SCP antibodies, or in therapeutic compositions containing such proteins and/or antibodies. Also provided are transgenic non-human mammals that express, or fail to express (e.g., knock-out), the invention protein.

Antibodies that are immunoreactive with invention SMDP and/or SCP proteins are also provided. These antibodies are useful in diagnostic assays to determine levels of SMDP and/or SCP proteins present in a given sample, e.g., tissue samples, Western blots, and the like. The antibodies can also be used to purify SMDP and/or SCP proteins from crude cell extracts and the like. Moreover, these antibodies are considered therapeutically useful to modulate the biological effect of SMDP and/or SCP proteins in vivo.

Also provided are bioassays for identifying compounds that modulate the activity of invention SMDP and/or SCP proteins. Methods and diagnostic systems for determining the levels of SMDP and/or SCP protein in various tissue samples are also provided. These diagnostic methods can be used for monitoring the level of therapeutically administered SMDP and/or SCP or fragments thereof to facilitate the maintenance of therapeutically effective amounts. These diagnostic methods can also be used to diagnose physiological disorders that result from abnormal levels of SMDP and/or SCP.

Also provided are systems using invention SMDPs, SCPs, or functional fragments thereof, or other protein-degradation binding domains, for targeting any desired protein for ubiquitination and degradation, thus enabling novel gene discovery through functional genomics strategies or providing the basis for ablating target proteins involved in diseases for therapeutic purposes.

In addition, compositions and methods are provided for ubiquitin-independent degradation of a target protein mediated by ornithine decarboxylase (ODC). Therefore, according to one embodiment of the invention, an isolated polynucleotide is provided that comprises a promoter sequence operably linked to a sequence that encodes a chimeric protein that comprises (a) a target-protein binding domain operatively linked to (b) a protein-degradation binding domain of ODC. Binding of the target-protein binding domain of the chimeric protein to a target protein in a cell induces degradation of the target protein in the cell. According to one embodiment, such a protein-degradation binding domain is an ODC C-terminal region polypeptide, including, but not limited to, a human ODC C-terminal region polypeptide. The ODC C-terminal region polypeptide may be a full-length ODC polypeptide or less than full length. According to another embodiment, the chimeric protein further comprises a linker sequence, for example, a flexible linker sequence, between the target-protein binding domain and the protein-degradation binding domain of ornithine decarboxylase. Examples of such flexible linker sequences include but are not limited to residues 31 to 94 of a Bcl-2 protein, a Gly-Gly-Pro tripeptide, and [Gly-Gly-Gly-Gly-Ser]₃. Thus, for example, the chimeric protein may comprise, in order from N-terminus to C-terminus, (a) a target-protein binding domain, (b) a flexible linker sequence, and (b) a protein-degradation binding domain of ornithine decarboxylase. According to another embodiment, the chimeric protein further comprises an epitope tag sequence. According to another embodiment of the invention, an isolated polynucleotide is provided that comprises: a first promoter sequence operably linked to a sequence that encodes a chimeric protein that comprises a target-protein binding domain operatively linked to a protein-degradation binding domain of ODC; and a second promoter sequence operably linked to a sequence that encodes an antizyme protein. Such an antizyme protein may be, for example, a human antizyme protein, including, but not limited to, a full-length antizyme protein. According to another embodiment of the invention, pharmaceutical compositions are provided that comprise one or more of the polynucleotides described above and a pharmaceutically acceptable carrier. According to another embodiment of the invention, such pharmaceutical compositions further comprising one or more polyamines. According to another embodiment of the compositions of the invention include, but are not limited to, cells comprising such isolated polynucleotides, including animals, such as mice, comprising such cells. According to another embodiment, kits are provided comprising: (a) a composition comprising an isolated polynucleotide that comprises a promoter sequence operably linked to a sequence that encodes a chimeric protein that comprises a target-protein binding domain operatively linked to a protein-degradation binding domain of ornithine decarboxylase, wherein binding of the target-protein binding domain of the chimeric protein to a target protein in a cell induces degradation of the target protein in the cell; (b) a composition comprising an isolated polynucleotide that comprises a promoter sequence operably linked to a sequence that encodes an antizyme protein; and (c) instructions for use.

According to another embodiment of the invention, isolated chimeric proteins are provided that comprise a target-protein binding domain operatively linked to a protein-degradation binding domain of ornithine decarboxylase, wherein binding of the target-protein binding domain of the chimeric protein to a target protein in a cell induces degradation of the target protein in the cell. Such chimeric proteins may comprise a linker sequence and an epitope tag, for example, as described above. According to another embodiment of the invention, pharmaceutical compositions are provided that comprise one or more such chimeric proteins and a pharmaceutically acceptable carrier. Such pharmaceutical compositions may also optionally comprise one or more polyamines.

According to another embodiment of the invention, methods are provided for degrading a target protein in a cell. Such methods comprise providing in a cell an isolated chimeric protein that comprises a target-protein binding domain operatively linked to a protein-degradation binding domain of ornithine decarboxylase, wherein binding of the target-protein binding domain of the chimeric protein to a target protein in the cell induces degradation of the target protein. According to one embodiment of such a method, the isolated chimeric polypeptide is provided in the cell by expressing in the cell a polynucleotide that comprises a promoter sequence operably linked to a sequence that encodes the chimeric protein, as described above. According to another embodiment of such a method, the isolated chimeric polypeptide and antizyme are provided in the cell by expressing in the cell (a) a first polynucleotide that comprises a first promoter sequence operably linked to a sequence that encodes the chimeric protein, and (b) a second polynucleotide that comprises a second promoter sequence operably linked to a sequence that encodes the antizyme protein. According to another embodiment of such a method, the isolated chimeric protein and the antizyme protein are provided in the cell by expressing in the cell a polynucleotide that comprises a first promoter sequence operably linked to a sequence that encodes the chimeric protein and a second promoter sequence operably linked to a sequence that encodes the antizyme protein. Thus, the sequences encoding the chimeric protein and the antizyme protein may be provided on one or more than one polynucleotide (e.g., vector) sequences. Such methods may further comprise contacting the cell with a composition comprising a polyamine, including, but not limited to, spermine, spermidine, putrescine, and analogs thereof.

According to another embodiment of the invention, method of identifying a phenotype of a target protein in a cell are provided that comprise (a) providing in the cell an isolated chimeric protein that comprises a target-protein binding domain operatively linked to a protein-degradation binding domain of ornithine decarboxylase, wherein binding of the target-protein binding domain of the chimeric protein to the target protein in the cell induces degradation of the target protein, and (b) observing a change of phenotype of the cell.

According to another embodiment of the invention, methods are provided for treating a patient having a disease characterized by expression of a target protein in a cell of the patient, the method comprising providing in the cell an isolated chimeric protein that comprises a target-protein binding domain operatively linked to a protein-degradation binding domain of ornithine decarboxylase, wherein binding of the target-protein binding domain of the chimeric protein to the target protein in the cell induces degradation of the target protein.

According to another embodiment of the invention, methods are provided for identifying a polynucleotide that encodes a target-protein binding domain that binds a target protein comprising: (a) expressing in the cell a vector that comprises a promoter sequence operably linked to a protein-coding sequence that comprises (i) a test polynucleotide sequence, and (ii) a polynucleotide sequence that encodes a protein-degradation binding domain of ornithine decarboxylase, and (b) observing a change of phenotype of the cell, wherein the change of phenotype indicates that the test polynucleotide sequence encodes the target-protein binding domain and that binding of the target-protein binding domain to the target protein in the cell induces degradation of the target protein.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows an amino acid sequence comparison of SIP-L (SEQ ID NO:4) and SIP-S (SEQ ID NO:6).

FIG. 2 shows the Destruction-box amino acid consensus sequence of SAD.

FIG. 3 shows the mapping of Siah-APC interaction domains as described in Example 12.

FIG. 4 shows the results of the cell proliferation functional assay of SIP/Siah interaction described in Example 7.

FIGS. 5A and 5B show in vitro and in vivo interaction assays of Siah-1 and SIP-L as described in Examples 8 and 9, respectively.

FIGS. 6A and 6B show the mapping of SKP1, SIP-L, SAF-1 and SAD interaction domains as described in Example 13.

FIG. 7 shows the effect of Siah-1 overexpression on stability of β-catenin.

FIG. 8 shows a diagram of how an invention SIP communicates with the protein ubiquitination machinery.

FIG. 9 shows a general diagram of an invention method for inducing targeted degradation of proteins using SIP, exemplified in Example 15.

FIG. 10 shows the results of the SIP-mediated degradation of the target TRAF6 protein, set forth in Example 15.

FIG. 11A shows a model for antizyme-dependent targeted protein degradation by ODC-conjugated proteins. FIG. 11B shows the amino acid sequence of an ODC-fusion protein (SEQ ID NO:50).

FIG. 12 shows targeted degradation of TRAF6. HEK293T cells were transiently transfected with plasmids encoding HA-TRAF6, HA-TRAF2, ODC, ODC-TRAF6C, ODC-RANK peptide, ODC-CD40CT or myc-antizyme in various combinations, as indicated. After 24 h, cell lysates were prepared and analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotted using antibodies specific for hemaglutinin (HA) (TRAF6) or Myc (ODC or antizyme). The levels of TRAF6 mRNA were measured by Northern blot (mRNA).

FIG. 13 shows additional examples of ODC-adapter-induced degradation of target protein(s). FIG. 13 A shows antizyme-dependent targeted degradation of retinoblastoma (Rb) by ODC-E7 peptide. HEK293T cells were transiently transfected with plasmid encoding HA-Rb, ODC, ODC-E7 peptide or myc-antizyme in various combinations, as indicated. FIG. 13B shows antizyme-independent targeted degradation of Cdk2 by ODC-p21waf-1. HEK293T cells were transiently transfected with plasmid encoding myc-Cdk2, ODC, ODC-p21waf-1 or myc-antizyme in various combinations, as indicated. FIG. 13C shows antizyme-independent targeted degradation of IKKβ by ODC-IKKβ (leucine-zipper domain). HEK293T cells were transiently transfected with plasmid encoding HA-IKKβ, ODC, ODC-IKKβ-LZ or myc-antizyme in various combinations, as indicated. After 24 h, cell lysates were prepared and analyzed by SDS-PAGE and immunoblotted using antibodies specific for Rb, Cdk2, IKKβ or HSC70 (as a control).

FIG. 14 shows analysis of interactions of ODC-TRAF6C and TRAF6. HEK293T cells were transiently transfected with plasmids encoding hemaglutinin (HA)-tagged TRAF6 and ODC, ODC-TRAF6C peptide or antizyme in various combinations, as indicated. After 24 h, 10 μM MG132 was added into culture media, and the cells were incubated another 6 hours. Lysates were subjected to immunoprecipitation using anti-myc monoclonal antibody-conjugated beads. The immunoprecipitates were analyzed by SDS-PAGE and immunoblotted using an anti-HA monoclonal antibody with ECL-based detection. As a control, 0.1 volume of input cell lysate was loaded directly in the same gel (Input).

FIG. 15 shows that targeted degradation of TRAF6 by ODC-RANK peptide is proteasome-dependent. HEK293T cells were transiently transfected with plasmid encoding HA-TRAF6, ODC-RANK peptide or myc-antizyme in various combinations, as indicated. After 24 h, cells were either untreated, treated with 1 μM MG132 (MG132), 1 nM Epoximycine (Epox.), 10 μM Lactastacine (Lact.) or 1 μM Trypsin inhibitor (Tryp.) for 6 hours. Cell lysates were prepared and analyzed by SDS-PAGE and immunoblotted using antibodies specific for HA.

FIG. 16 shows pulse-chase analysis of ectopically expressed HA-tagged TRAF6. HEK239T cells were transiently co-transfected with plasmids encoding HA-TRAF6 and ODC-RANK peptide, with or without myc-antizyme. After 24 hours, cells were pulse-labeled with ³⁵S-methionine and cysteine, and then chased with media lacking the labeled amino acids. Cells were lysed at the indicated times, and the expressed HA-TRAF6 was recovered by immunoprecipitation via a HA epitope tag. Immunoprecipitated HA-TRAF6 was subjected to SDS-PAGE and dried gels were analyzed with a PhosphorImager. Data from pulse-chase analysis is presented as the average±SD from duplicate experiments.

FIG. 17 shows functional analysis using ODC-E7 peptide. FIG. 17A shows degradation of endogenous Rb protein by ODC-E7. HEK293T cells were transiently transfected with plasmid encoding ODC, ODC-E7 peptide or myc-Antizyme in various combinations, as indicated. After 48 h, lysates were prepared and subjected to immunoprecipitation using anti-Rb monoclonal antibody. The immunoprecipitates were analyzed by SDS-PAGE and immunoblotting using an anti-Rb monoclonal antibody. FIG. 17B shows the effect of ODC-E7 on E2F reporter activity. HEK293T cells were transiently transfected with a reporter gene plasmid that contains a E2F responsive element cloned upstream of a luciferase reporter gene, together with pCMVβ-gal as a transfection-efficiency control, and plasmids encoding ODC, ODC-E7 or Antizyme in various combinations, as indicated in FIG. 17A. Luciferase activity was measured in cell lysates 24 hr later, and normalized relative to β-galactosidase (mean±std. dev.; n=3).

FIG. 18 shows the effect of ODC-RANK peptide and ODC-TRAF6C on IL-1-induced NFκB reporter activity. HEK293T cells were transiently transfected with a reporter gene plasmid that contains an NFκB responsive element cloned upstream of a luciferase reporter gene, together with pCMVβ-gal as a transfection-efficiency control, and plasmids encoding ODC, ODC-TRAF6C, ODC-RANK peptide, or Antizyme in various combinations, as indicated. After 24 hours, cells were treated with 50 ng/ml IL-1 or 10 ng/ml TNFα for an additional 24 hours. Luciferase activity was measured in cell lysates and normalized relative to β-galactosidase (mean±std. dev.; n=3).

FIG. 19 shows the requirement of FL for targeted degradation of Rb by ODC-F7 peptide. HEK293T cells were transiently transfected with 0.2 μg of plasmid encoding HA-Rb (0.5 μg), ODC (0.5 μg), ODC-E7 peptide (0.5 μg), ODC-E7 peptide plus FL (GGGGS) (0.5 μg), or myc-AZ (0.5 μg), in various combinations as indicated (total DNA amount normalized). After 24 hours (h), cell lysates were prepared from duplicate dishes of transfectants, normalized for total protein content (20 μg per lane), and analyzed by SDS/PAGE/immunoblotting using antibodies specific for HA (Rb), Myc (ODC or AZ), or HSC70 (as a control) with enhanced-chemiluminescence-based detection.

FIG. 20 shows selective degradation of TRAF6 but not TRAF2 by ODC chimeric fusion polypeptides. Duplicate cultures of HEK293T cells were transiently transfected with 0.2 μg of plasmid encoding HA-TRAF6 (0.5 μg) (Upper), HA-TRAF2 (0.5 μg) (Lower), ODC (0.5 μg), ODC-C-TRAF6 (0.5 μg), ODC-RANKp (0.5 μg), or myc-AZ (0.5 μg), in various combinations as indicated (total DNA amount normalized). After 24 h, cell lysates were prepared for analysis of either polypeptide or mRNA. Immunoblot analysis was performed by using detergent lysates normalized for total protein content (20 μg per lane) by SDS/PAGE/immunoblotting using antibodies specific for HA (TRAF6; TRAF2), Myc (ODC or AZ) with enhanced-chemiluminescence-based detection. The relative levels of TRAF6 mRNA were analyzed by Northern blotting using sample normalized for total RNA content (10 μg per lane). Ethidium bromide staining verified loading of equivalent amounts of RNA for each sample.

FIG. 21 shows AZ-dependent, proteasome-dependent degradation of target polypeptide induced by ODC chimeric fusion polypeptide. (A) Proteasome-dependent degradation of TRAF6 by ODC-RANKp peptide. HEK293T cells were transiently transfected with plasmids encoding HA-TRAF6 (0.5 μg), ODC-RANKp (0.5 μg), or myc-AZ (0.5 μg) in various combinations, as indicated (total DNA amount normalized). After 24 h, cells were cultured with or without 1 μM MG132, 1 mM epoximycin (Epox), 10 μM lactacystin (Lact), or 1 μM Trypsin inhibitor (Tryp) for 6 h. Cell lysates were prepared from duplicated dishes of transfectants, normalized for total protein content (20 μg per lane), and analyzed by SDS/PAGE/immunoblotting using antibodies specific for HA. (B) Pulse-chase analysis of TRAF6 protein-degradation rate in ODC-RANKp transfected cells. HEK239T cells were transiently cotransfected with plasmids encoding HA-TRAF6 and ODC-RNAKp, with or without myc-AZ. After 24 h, cells were pulse-labeled with [³⁵S]methionine and [³⁵S]cysteine in methionine/cysteine-free medium, and chased with media lacking the labeled amino acids. Cells were lysed at the indicated times, and HA-TRAF6 was recovered by immunoprecipitation by using HA antibody. Immune complexes were subjected to SDS/PAGE, and dried gels were analyzed by PhosphorImager (Upper). Data from pulse-chase analysis are presented as the average (±SE) from duplicate experiments (Lower). The blots shown are representative of duplicate experiments. (C) Pulse-chase analysis of IKK^(β) protein-degradation rate. HEK293T cells were transiently cotransfected with plasmids encoding HA-IKK^(β), with ODC or ODC-IKK^(β). After 24 h, cells were pulse-labeled with [³⁵S]methionine and [³⁵S]cysteine in methionine/cystein-free medium and chased with media lacking the labeled amino acids. Cells were lysed at the indicated times, and HA-IKK^(β) was recovered by immunoprecipitation by using HA antibody. Immune complexes were subjected to SDS/PAGE, and dried gels were analyzed by PhosphorImager (Upper). Data from pulse-chase analysis are presented as the average (±SE) from duplicate experiments (Lower). The blots shown are representative of duplicate experiments. (D) The analysis of Flag-Cdk2 protein-degradation rate after cycloheximide treatment. HEK293T cells (six wells) were transiently cotransfected with plasmids encoding Flag-Cdk2 (0.5 μg), with ODC (2 μg) or ODC-p21 (2 μg). After 24 h, cells were treated with cycloheximide (50 μg/ml), lysed at the indicated times and analyzed by SDS/PAGE/immunoblotting using antibodies specific for Flag (Upper). Data are presented as the average (±SE) from duplicate experiments (Lower). The blots shown are representative of duplicate experiments.

FIG. 22 shows the functional ablation of endogenous TRAF6 by ODC/AZ system. HEK293T cells were transiently transfected with a reporter gene plasmid (0.1 μg) that contains a NFκB-responsive element cloned upstream of a luciferase reporter gene, with 0.01 μg of pCMV^(β)-gal as a transfection-efficiency control and 0.1 μg of the indicated plasmids encoding ODC, ODC-TRAF6C, ODC-RANKp, or AZ, in various combinations as indicated (total DNA amount normalized). After 24 h, cells were treated with 50 ng/ml IL-1 (Left) or 10 ng/ml TNFα (Right) for an additional 24 h, and luciferase activity was measured in cell lysates and normalized relative to beta-galactosidase (mean±SD; n=3).

FIG. 23 shows the ablation of endogenous Rb expression by using ODC/AZ system. (A) Scheme for E2F activation by AZ-assisted degradation of Rb polypeptides by ODC-E7p. (B) Degradation of endogenous Rb polypeptide by ODC-E7p. HEK293T cells (100-mm dish) were transiently transfected with 2 μg of plasmid encoding ODC (2 μg), ODC-E7p (2 μg), or myc-AZ (2 μg) in various combinations, as indicated (total DNA amount normalized). After 48 h, lysates were normalized for total protein content and subjected to immunoprecipitation by using 1 μg of anti-Rb monoclonal antibody. The resulting immune complexes were analyzed by SDS/PAGE/immunoblotting using an anti-Rb monoclonal antibody with enhanced-chemiluminescence-based detection. (C) Effect of ODC-E7p on E2F transcriptional activity. HEK293T cells were transiently transfected with a reporter gene plasmid (0.1 μg) that contains an E2F responsive element cloned upstream of a luciferase reporter gene, 0.01 μg of pCMV^(β)-galactosidase as an transfection-efficiency control, and 0.1 μg of the indicated plasmids encoding ODC, ODC-E7p, or AZ, in various combinations as indicated (total DNA amount normalized). Luciferase activity was measured in cell lysates 24 h later and normalized relative to beta-galactosidase (mean±SD; n=3).

DETAILED DESCRIPTION OF THE INVENTION

Siah-Mediated Protein Destruction by a Ubiquitin-Dependent Mechanism

In accordance with the present invention, there are provided isolated nucleic acids, which encode novel mammalian Siah-Mediated-Degradation-Proteins (SMDPs) and/or SCF-Complex-Proteins (SCPs), and functional fragments thereof. SMDPs are involved in the Siah-mediated protein degradation pathways and SCPs are involved in SCF-mediated protein degradation pathways. In some instances, these two pathways for protein degradation may operate in collaboration, particularly in cases where proteins have been identified that physically link SMDPs to SCPs. Invention SMDPs and/or SCPs are contemplated herein to regulate protein degradation, either by activating or inhibiting such protein degradation.

As used herein, invention SMDPs are proteins that participate in the Siah-mediated protein degradation pathway. The term “Siah” refers to the mammalian family of proteins encoded by at least two genes referred to as SIAH1 and SIAH2 (Hu, G. et al., 1997, Genomics 46:103-111). Like their Drosophila counterpart protein Sina, the Siah-1 and Siah-2 proteins bind ubiquitin conjugating enzymes (UBCs) via an N-terminal RING domain and target other proteins for degradation.

As used herein, invention SCPs are proteins that participate in the Skp-1, Cullin, F-box (SCF) protein degradation pathway. These proteins can be components of SCF complexes or proteins that associate with SCF complexes. In some instances an invention protein may fulfill the requirements of both a SMDP and a SCP.

Using yeast two-hybrid screening methods, targets of Siah-mediated protein degradation have been identified demonstrating the involvement of Siah and other inventions SMDPs and/or SCPs in pathways involved in cell growth regulation in cancers. For example, evidence is provided herein demonstrating that Siah-1 interacts indirectly with SCF complexes through associations with an invention SIP protein. Siah-1 has also been found to be an important regulator of cell growth, through its effects on ubiquitination and degradation of β-catenin and possibly other target proteins including an invention protein SAD.

Thus far, the only reported target of Siah-mediated degradation is DCC (Hu, G. et al., 1997, Genes & Dev., 11:2701-2714), a putative tumor suppressor protein encoded by a gene which is commonly disrupted in colon cancers (Fearon, E. R. et al., 1990, Science, 247:49-56). The involvement of DCC in colon cancers however has recently been questioned, and it appears that a different gene located near DCC on 18q21 is the primary target of deletions in this chromosomal region (Fearon, E. R. et al., 1990, supra). However, the DCC protein has recently been shown to deliver either pro-apoptotic or anti-apoptotic signals, depending on whether it is complexed with its ligand Netrin. These observations suggest that deletion or inactivation of DCC could potentially contribute to tumorigensis by removing a pro-apoptotic influence from cells.

Another connection between the Siah-family of proteins and tumor suppressor genes has been found for p53. For example, the Siah-1 gene of mice was found among a group of immediate-early genes induced by p53 using a hemopoietic cell line as a model for p53-induced cell cycle arrest and apoptosis (Amson, R. B. et al., 1996, PNAS USA 93:3953-3957). Expression of Siah-1 was also indirectly correlated with increased apoptosis in tumor xenograph experiments, suggesting that Siah-1 could function as a tumor suppressor in some contexts (Nemani, M. et al., 1996, Proc. Natl. Sci. USA 93:9039-9042).

It has also been found that Siah-1 over-expression can induce cell cycle arrest independently of apoptosis in epithelial cancer cells (Matsuzawa, et al., 1998, EMBO J. 17(10):2736-2747). Moreover, UV-irradiation at subapoptotic doses was shown to induce Siah-1 gene expression in MCF7 breast cancer cells and to promote cell cycle arrest. These and other data have implicated Siah-1 in a p53-inducible pathway for cell cycle arrest which runs parallel to the well-studied p21-Waf1 pathway (Matsuzawa, et al. 1998, supra).

The phrase “SMDP and/or SCP” refers to substantially pure native SMDP and/or SCP, or recombinantly produced proteins, including naturally occurring allelic variants thereof encoded by mRNA generated by alternative splicing of a primary transcript, and further including fragments thereof which retain at least one native biological activity, such as immunogenicity, the ability to bind to a SMDP and/or SCP, and the like. Exemplary SMDPs and/or SCPs referred to herein include amino acid sequences set forth in SEQ ID Nos:2 (Siah-1α), 4 (SIP-L), 6 (SIP-S), 8 (SAF-1α), 10 (SAF-1), 12 (SAF-2) and 14 (SAD). Invention isolated SMDPs and/or SCPs are substantially pure and free of cellular components and/or contaminants normally associated with a native in vivo environment.

As used herein, the term “Siah-1α” refers to a splice-variant member of the mammalian, preferably human, Siah-family of proteins. The invention Siah-1α protein, or functional fragment thereof, is characterized by having the ability to bind to at least one or more of the proteins selected from APC (Kinzler K. W., et al., 1996, Cell, 87(2):159-170); BAG-1 (Takayama et al., 1995, Cell, 80(2):279-284); SIP-L; SIP-S; or other Siah proteins, such as Siah-1. Thus, homodimers of Siah-1α are contemplated herein. Invention Siah-1α proteins differ from Siah-1β (set forth as SIAH-1 in Hu et al., 1997, Genomics, 46:103-111) by containing an additional 16 amino acids at the amino-terminus. Thus, preferred invention Siah-1α proteins, and fragments thereof, comprise at least a portion of the 16 N-terminal amino acids of SEQ ID NO:2. A particularly preferred Siah-1α protein is set forth in SEQ ID NO:2.

In accordance with another embodiment of the invention, Siah-1 has been found to interact with an invention protein referred to herein as the “SIP” family. As used herein, the term “SIP” refers to any species, preferably mammalian, more preferably human, Siah-1-Interacting Protein (SIP). The invention SIP proteins, or functional fragments thereof, are characterized by having the ability to bind to at least one or more of the proteins selected from Siah-1, Skp1, or other SIP proteins. Thus, homodimers of invention SIP proteins are contemplated herein. The SIP gene has been found to encode at least two proteins through alternative mRNA splicing: SIP-L (L, for long; SEQ ID NO:4), and SIP-S(S, for short; SEQ ID NO:6). A sequence comparison of SIP-L to SIP-S is set forth in FIG. 1. To further identify potential targets of Siah-1-mediated ubiquitin/proteasome protein degradation, yeast two-hybrid screens of cDNA libraries were performed using the invention human SIP-L protein (SEQ ID NO:4) as a bait. Such screen resulted in the identification of Skp1 (Zhang et al., 1995, Cell, 82(6):915-925).

As shown in FIG. 8, an invention SIP protein binds simultaneously to Siah and Skp, proteins known to bind directly or indirectly, respectively, to ubiquitin-conjugating enzymes (E2s). Therefore, in accordance with the present invention, this characteristic of SIP is useful for methods for targeting desired proteins for degradation, via a ubiquitin/proteosome-dependent mechanism (see, e.g., Example 15).

In accordance with another embodiment of the invention, using a yeast two-hybrid screen with Skp1 as bait (set forth in the Examples), two additional invention SMDP and/or SCP proteins were identified as Skp1-interacting proteins, which are referred to herein as SAF-1 and SAD. As used herein the term “SAF-1” refers to Skp1-Associated F-box protein-1. The invention SAF-1 proteins, or functional fragments thereof, are characterized by having the ability to bind to at least one or more of the proteins selected from Skp1, SIP, such as SIP-L, or SAD. Invention SAF-1 proteins are further characterized as containing an “F-box” amino acid domain. Exemplary SAF-1 proteins include SAF-1α (SEQ ID NO:8) and SAF-1 (SEQ ID NO:10). An exemplary F-box domain is set forth as amino acids 256-296 of SEQ ID NO:8 and amino acids 335-375 of SEQ ID NO:10 (see FIG. 6). SAF-1 beta has the same F-Box as alfa, the location is in amino acids 335-375. In accordance with the present invention, a homologue of SAF-1 protein has also been identified in the NCBI BLAST data base (Human DNA sequence from clone 341E18 on chromosome 6p11.2-12.3, AL031178) which shares significant homology with F-box domain of SAF-1. The invention homolog is referred to herein as SAF-2 and is set forth in SEQ ID Nos:11 and 12.

As used herein the term “SAD” refers to Skp1-Associated Destruction-box protein. The invention SAF-1 proteins, or functional fragments thereof, are characterized by having the ability to bind to at least one or more of the proteins selected from Skp1, SIP, such as SIP-L, or SAF-1. It is also contemplated herein that SAD has the ability to bind to SAF-2. Invention SAD proteins are further characterized as containing an “D-box” (Destruction-box) amino acid domain. An exemplary SAD protein is set forth herein as SEQ ID NO:14. As used herein, the D-box domain comprises the consensus amino acid sequence -DSGX₁X₂S—, wherein X₁ is preferably selected from a hydrophobic amino acid, such as Y, I, L, M, F, W, or V; and X₂ is any amino acid (see FIG. 2). A preferred D-box domain comprises the sequence set forth as amino acids 144-149 of SEQ ID NO:14.

Thus, exemplary functional fragments of an invention SAD protein comprise at least amino acids 144-149 of SEQ ID NO:14. Also contemplated herein are functional fragments of inventions SAD proteins that bind to a SIP protein, and preferably comprise at least amino acids 360-447 of SEQ ID NO:14. Functional fragments of inventions SAD proteins that bind to a Skp1 protein preferably comprise at least amino acids 128-359 of SEQ ID NO:14. Functional fragments of inventions SAD proteins that bind to a SAF-1 protein preferably comprise at least amino acids 1-127 of SEQ ID NO:14.

The nucleic acid molecules described herein are useful for producing invention proteins, when such nucleic acids are incorporated into a variety of protein expression systems known to those of skill in the art. In addition, such nucleic acid molecules or fragments thereof can be labeled with a readily detectable substituent and used as hybridization probes for assaying for the presence and/or amount of an invention SMDP and/or SCP gene or mRNA transcript in a given sample. The nucleic acid molecules described herein, and fragments thereof, are also useful as primers and/or templates in a PCR reaction for amplifying genes encoding invention proteins described herein.

The term “nucleic acid” (also referred to as polynucleotides) encompasses ribonucleic acid (RNA) or deoxyribonucleic acid (DNA), probes, oligonucleotides, and primers. DNA can be either complementary DNA (cDNA) or genomic DNA, e.g. a gene encoding a SMDP and/or SCP. One means of isolating a nucleic acid encoding an SMDP and/or SCP polypeptide is to probe a mammalian genomic library with a natural or artificially designed DNA probe using methods well known in the art. DNA probes derived from the SMDP and/or SCP gene are particularly useful for this purpose. DNA and cDNA molecules that encode SMDP and/or SCP polypeptides can be used to obtain complementary genomic DNA, cDNA or RNA from mammalian (e.g., human, mouse, rat, rabbit, pig, and the like), or other animal sources, or to isolate related cDNA or genomic clones by the screening of cDNA or genomic libraries, by methods described in more detail below. Examples of nucleic acids are RNA, cDNA, or isolated genomic DNA encoding an SMDP and/or SCP polypeptide. Such nucleic acids may include, but are not limited to, nucleic acids comprising substantially the same nucleotide sequence as set forth in SEQ ID Nos:1 (Siah-1), 3 (SIP-L), 5 (SIP-S), 7 (SAF-1α), 9 (SAF-1β), 11 (SAF-2) and 13 (SAD).

Use of the terms “isolated” and/or “purified” in the present specification and claims as a modifier of DNA, RNA, polypeptides or proteins means that the DNA, RNA, polypeptides or proteins so designated have been produced in such form by the hand of man, and thus are separated from their native in vivo cellular environment, and are substantially free of any other species of nucleic acid or protein. As a result of this human intervention, the recombinant DNAs, RNAs, polypeptides and proteins of the invention are useful in ways described herein that the DNAs, RNAs, polypeptides or proteins as they naturally occur are not.

Invention proteins can be obtained from any species of organism, such as prokaryotes, eukaryotes, plants, fungi, vertebrates, invertebrates, and the like. A particular species can be d mammalian, As used herein, “mammalian” refers to a subset of species from which an invention SMDP and/or SCP is derived, e.g., human, rat, mouse, rabbit, monkey, baboon, bovine, porcine, ovine, canine, feline, and the like. A preferred SMDP and/or SCP herein, is human SMDP and/or SCP.

In one embodiment of the present invention, cDNAs encoding the invention SMDPs and/or SCPs disclosed herein comprise substantially the same nucleotide sequence as the coding region set forth in any of SEQ ID NOs:1, 3, 5, 7, 9, 11 and 13. Preferred cDNA molecules encoding the invention proteins comprise the same nucleotide sequence as as the coding region set forth in any of SEQ ID NOs:1, 3, 5, 7, 9, 11 and 13.

As employed herein, the term “substantially the same nucleotide sequence” refers to DNA having sufficient identity to the reference polynucleotide, such that it will hybridize to the reference nucleotide under moderately stringent hybridization conditions. In one embodiment, DNA having substantially the same nucleotide sequence as the reference nucleotide sequence encodes substantially the same amino acid sequence as that set forth in any of SEQ ID Nos:2, 4, 6, 8, 10, 12 or 14. In another embodiment, DNA having “substantially the same nucleotide sequence” as the reference nucleotide sequence has at least 60% identity with respect to the reference nucleotide sequence. DNA having at least 70%, more preferably at least 90%, yet more preferably at least 95%, identity to the reference nucleotide sequence is preferred.

This invention also encompasses nucleic acids which differ from the nucleic acids shown in SEQ ID NOs:1, 3, 5, 7, 9, 11 and 13, but which have the same phenotype. Phenotypically similar nucleic acids are also referred to as “functionally equivalent nucleic acids”. As used herein, the phrase “functionally equivalent nucleic acids” encompasses nucleic acids characterized by slight and non-consequential sequence variations that will function in substantially the same manner to produce the same protein product(s) as the nucleic acids disclosed herein. In particular, functionally equivalent nucleic acids encode polypeptides that are the same as those encoded by the nucleic acids disclosed herein or that have conservative amino acid variations. For example, conservative variations include substitution of a non-polar residue with another non-polar residue, or substitution of a charged residue with a similarly charged residue. These variations include those recognized by skilled artisans as those that do not substantially alter the tertiary structure of the protein.

Further provided are nucleic acids encoding SMDP and/or SCP polypeptides that, by virtue of the degeneracy of the genetic code, do not necessarily hybridize to the invention nucleic acids under specified hybridization conditions. Preferred nucleic acids encoding the invention SMDPs and/or SCPs are comprised of nucleotides that encode substantially the same amino acid sequence as set forth in SEQ ID Nos:2, 4, 6, 8, 10, 12 or 14.

Thus, an exemplary nucleic acid encoding an invention SMDP and/or SCP may be selected from: (a) DNA encoding the amino acid sequence set forth in SEQ ID Nos:2, 4, 6, 8, 10, 12 or 14, (b) DNA that hybridizes to the DNA of (a) under moderately stringent conditions, wherein said DNA encodes biologically active SMDP and/or SCP, or (c) DNA degenerate with respect to either (a) or (b) above, wherein said DNA encodes biologically active SMDP and/or SCP.

Hybridization refers to the binding of complementary strands of nucleic acid (i.e., sense:antisense strands or probe:target-DNA) to each other through hydrogen bonds, similar to the bonds that naturally occur in chromosomal DNA. Stringency levels used to hybridize a given probe with target-DNA can be readily varied by those of skill in the art.

The phrase “stringent hybridization” is used herein to refer to conditions under which polynucleic acid hybrids are stable. As known to those of skill in the art, the stability of hybrids is reflected in the melting temperature (T_(m)) of the hybrids. In general, the stability of a hybrid is a function of sodium ion concentration and temperature. Typically, the hybridization reaction is performed under conditions of lower stringency, followed by washes of varying, but higher, stringency. Reference to hybridization stringency relates to such washing conditions.

As used herein, the phrase “moderately stringent hybridization” refers to conditions that permit target-DNA to bind a complementary nucleic acid that has about 60% identity, preferably about 75% identity, more preferably about 85% identity to the target DNA; with greater than about 90% identity to target-DNA being especially preferred. Preferably, moderately stringent conditions are conditions equivalent to hybridization in 50% formamide, 5× Denhart's solution, 5×SSPE, 0.2% SDS at 42° C., followed by washing in 0.2×SSPE, 0.2% SDS, at 65° C.

The phrase “high stringency hybridization” refers to conditions that permit hybridization of only those nucleic acid sequences that form stable hybrids in 0.018M NaCl at 65° C. (i.e., if a hybrid is not stable in 0.018M NaCl at 65° C., it will not be stable under high stringency conditions, as contemplated herein). High stringency conditions can be provided, for example, by hybridization in 50% formamide, 5× Denhart's solution, 5×SSPE, 0.2% SDS at 42° C., followed by washing in 0.1×SSPE, and 0.1% SDS at 65° C.

The phrase “low stringency hybridization” refers to conditions equivalent to hybridization in 10% formamide, 5× Denhart's solution, 6×SSPE, 0.2% SDS at 42° C., followed by washing in 1×SSPE, 0.2% SDS, at 50° C. Denhart's solution and SSPE (see, e.g., Sambrook et al., Molecular Cloning A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1989) are well known to those of skill in the art as are other suitable hybridization buffers.

As used herein, the term “degenerate” refers to codons that differ in at least one nucleotide from a reference nucleic acid, e.g., SEQ ID NOs:1, 3, 5, 7, 9, 11 and 13, but encode the same amino acids as the reference nucleic acid. For example, codons specified by the triplets “UCU”, “UCC”, “UCA”, and “UCG” are degenerate with respect to each other since all four of these codons encode the amino acid serine.

Preferred nucleic acids encoding the invention polypeptide(s) hybridize under moderately stringent, preferably high stringency, conditions to substantially the entire sequence, or substantial portions (i.e., typically at least 15-30 nucleotides) of the nucleic acid sequence set forth in SEQ ID NOs:1, 3, 5, 7, 9, 11 and 13.

The invention nucleic acids can be produced by a variety of methods well-known in the art, e.g., the methods described herein, employing PCR amplification using oligonucleotide primers from various regions of SEQ ID NOs:1, 3, 5, 7, 9, 11 and 13, and the like.

In accordance with a further embodiment of the present invention, optionally labeled SMDP and/or SCP-encoding cDNAs, or fragments thereof, can be employed to probe library(ies) (e.g., cDNA, genomic, and the like) for additional nucleic acid sequences encoding novel mammalian SMDPs and/or SCPs. Construction of suitable mammalian cDNA libraries is well-known in the art. Screening of such a cDNA library is initially carried out under low-stringency conditions, which comprise a temperature of less than about 42° C., a formamide concentration of less than about 50%, and a moderate to low salt concentration.

Presently preferred probe-based screening conditions comprise a temperature of about 37° C., a formamide concentration of about 20%, and a salt concentration of about 5× standard saline citrate (SSC; 20×SSC contains 3M sodium chloride, 0.3M sodium citrate, pH 7.0). Such conditions will allow the identification of sequences which have a substantial degree of similarity with the probe sequence, without requiring perfect homology. The phrase “substantial similarity” refers to sequences which share at least 50% homology. Preferably, hybridization conditions will be selected which allow the identification of sequences having at least 70% homology with the probe, while discriminating against sequences which have a lower degree of homology with the probe. As a result, nucleic acids having substantially the same nucleotide sequence as SEQ ID NOs:1, 3, 5, 7, 9, 11 and 13 are obtained.

As used herein, a nucleic acid “probe” is single-stranded DNA or RNA, or analogs thereof, that has a sequence of nucleotides that includes at least 14, at least 20, at least 50, at least 100, at least 200, at least 300, at least 400, or at least 500 contiguous bases that are the same as (or the complement of) any contiguous bases set forth in any of SEQ ID NOs:1, 3, 5, 7, 9, 11 and 13. Preferred regions from which to construct probes include 5′ and/or 3′ coding regions of SEQ ID NOs:1, 3, 5, 7, 9, 11 and 13. In addition, the entire cDNA encoding region of an invention SMDP and/or SCP, or the entire sequence corresponding to SEQ ID NOs:1, 3, 5, 7, 9, 11 and 13, may be used as a probe. Probes may be labeled by methods well-known in the art, as described hereinafter, and used in various diagnostic kits.

It is understood that a SMDP and/or SCP-encoding nucleic acid molecule of the invention, as used herein, specifically excludes previously known nucleic acid molecules consisting of nucleotide sequences having identity with the SMDP and/or SCP-encoding nucleotide sequence (e.g., SEQ ID NO:NOs:1, 3, 5, 7, 9, 11, 13), such as Expressed Sequence Tags (ESTs), Sequence Tagged Sites (STSs) and genomic fragments, deposited in public databases such as the nr, dbest, dbsts, gss and htgs databases, which are available for searching at http://www.ncbi.nlm.nih.gov/blast/blast.cgi?Jform=0, using the program BLASTN 2.0.9 described by Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997).

In particular, a SMDP and/or SCP-encoding nucleic acid molecule specifically excludes nucleic acid molecules consisting of any of the nucleotide sequences having the Genbank (gb), EMBL (emb) or DDBJ (dbj) accession numbers described below. Similarly, a SMDP and/or SCP polypeptide fragment specifically excludes the amino acid fragments encoded by the nucleotide sequences having the GenBank accession numbers described below. GenBank accession numbers specifically excluded include NCBI ID: AA054272, AA258606, AA923663, AA418482, and AI167464. The human sequence referenced as GenBank accession No. AL031178 is also specifically excluded from an invention SMDP and/or SCP-encoding nucleic acid.

As used herein, the terms “label” and “indicating means” in their various grammatical forms refer to single atoms and molecules that are either directly or indirectly involved in the production of a detectable signal. Any label or indicating means can be linked to invention nucleic acid probes, expressed proteins, polypeptide fragments, or antibody molecules. These atoms or molecules can be used alone or in conjunction with additional reagents. Such labels are themselves well-known in clinical diagnostic chemistry.

The labeling means can be a fluorescent labeling agent that chemically binds to antibodies or antigens without denaturation to form a fluorochrome (dye) that is a useful immunofluorescent tracer. A description of immunofluorescent analytic techniques is found in DeLuca, “Immunofluorescence Analysis”, in Antibody As a Tool, Marchalonis et al., eds., John Wiley & Sons, Ltd., pp. 189-231 (1982), which is incorporated herein by reference.

In one embodiment, the indicating group is an enzyme, such as horseradish peroxidase (HRP), glucose oxidase, and the like. In another embodiment, radioactive elements are employed labeling agents. The linking of a label to a substrate, i.e., labeling of nucleic acid probes, antibodies, polypeptides, and proteins, is well known in the art. For instance, an invention antibody can be labeled by metabolic incorporation of radiolabeled amino acids provided in the culture medium. See, for example, Galfre et al., Meth. Enzymol., 73:3-46 (1981). Conventional means of protein conjugation or coupling by activated functional groups are particularly applicable. See, for example, Aurameas et al., Scand. J. Immunol., Vol. 8, Suppl. 7:7-23 (1978), Rodwell et al., Biotech., 3:889-894 (1984), and U.S. Pat. No. 4,493,795.

In accordance with another embodiment of the present invention, there are provided isolated mammalian Siah-Mediated-Degradation-Proteins (SMDPs) and/or SCF-Complex-Proteins (SCPs), and fragments thereof encoded by invention nucleic acid. The phrase “SMDP and/or SCP” refers to substantially pure native SMDP and/or SCP, or recombinantly produced proteins, including naturally occurring allelic variants thereof encoded by mRNA generated by alternative splicing of a primary transcript, and further including fragments thereof which retain at least one native biological activity, such as immunogenicity, the ability to bind to another member of the SMDP and/or SCP families, or to homodimerize. In another embodiment, SMDPs and/or SCPs referred to herein, are those polypeptides specifically recognized by an antibody that also specifically recognizes a SMDP and/or SCP (preferably human) including an amino acid sequence set forth in SEQ ID NOs:2, 4, 6, 8, 10, 12 and 14. Invention isolated SMDPs and/or SCPs are substantially pure and free of cellular components and/or contaminants normally associated with a native in vivo environment.

Presently preferred SMDPs and/or SCPs of the invention include proteins that comprise substantially the same amino acid sequences as the protein sequence set forth in SEQ ID NOs:2, 4, 6, 8, 10, 12 and 14, as well as biologically active, functional fragments thereof.

Those of skill in the art will recognize that numerous residues of the above-described sequences can be substituted with other, chemically, sterically and/or electronically similar residues without substantially altering the biological activity of the resulting receptor species. In addition, larger polypeptide sequences containing substantially the same sequence as amino acids set forth in SEQ ID NOs:2, 4, 6, 8, 10, 12 and 14 therein (e.g., splice variants) are contemplated.

As employed herein, the term “substantially the same amino acid sequence” refers to amino acid sequences having at least about 70% identity with respect to the reference amino acid sequence, and retaining comparable functional and biological activity characteristic of the protein defined by the reference amino acid sequence. Preferably, proteins having “substantially the same amino acid sequence” will have at least about 80%, more preferably 90% amino acid identity with respect to the reference amino acid sequence; with greater than about 95% amino acid sequence identity being especially preferred. It is recognized, however, that polypeptides (or nucleic acids referred to hereinbefore) containing less than the described levels of sequence identity arising as splice variants or that are modified by conservative amino acid substitutions, or by substitution of degenerate codons are also encompassed within the scope of the present invention.

The term “biologically active” or “functional”, when used herein as a modifier of invention SMDP and/or SCP(s), or polypeptide fragments thereof, refers to a polypeptide that exhibits functional characteristics similar to SMDP and/or SCP. For example, one biological activity of SMDP and/or SCP is the ability to bind, preferably in vivo, to at least one other member of the SMDP and/or SCP families of proteins, or to homodimerize, or to mediate protein degradation via an SFC complex as described herein. Such SMDP and/or SCP binding activity can be assayed, for example, using the methods described herein. Another biological activity of SMDP and/or SCP is the ability to act as an immunogen for the production of polyclonal and monoclonal antibodies that bind specifically to an invention SMDP and/or SCP. Thus, an invention nucleic acid encoding SMDP and/or SCP will encode a polypeptide specifically recognized by an antibody that also specifically recognizes the SMDP and/or SCP protein (preferably human) including the amino acid set forth in SEQ ID NOs:2, 4, 6, 8, 10, 12 and 14. Such immunologic activity may be assayed by any method known to those of skill in the art. For example, a test-polypeptide encoded by a SMDP and/or SCP cDNA can be used to produce antibodies, which are then assayed for their ability to bind to an invention SMDP and/or SCP protein including the sequence set forth in SEQ ID Nos:2, 4, 6, 8, 10, 12 or 14. If the antibody binds to the test-polypeptide and the protein including the sequence encoded by SEQ ID NOs:2, 4, 6, 8, 10, 12 or 14 with substantially the same affinity, then the polypeptide possesses the requisite immunologic biological activity.

The invention SMDPs and/or SCPs can be isolated by a variety of methods well-known in the art, e.g., recombinant expression systems described herein, precipitation, gel filtration, ion-exchange, reverse-phase and affinity chromatography, and the like. Other well-known methods are described in Deutscher et al., Guide to Protein Purification: Methods in Enzymology Vol. 182 (Academic Press, (1990)), which is incorporated herein by reference. Alternatively, the isolated polypeptides of the present invention can be obtained using well-known recombinant methods as described, for example, in Sambrook et al., supra., 1989).

An example of the means for preparing the invention polypeptide(s) is to express nucleic acids encoding the SMDP and/or SCP in a suitable host cell, such as a bacterial cell, a yeast cell, an amphibian cell (i.e., oocyte), or a mammalian cell, using methods well known in the art, and recovering the expressed polypeptide, again using well-known methods. Invention polypeptides can be isolated directly from cells that have been transformed with expression vectors as described below herein. The invention polypeptide, biologically functional fragments, and functional equivalents thereof can also be produced by chemical synthesis. For example, synthetic polypeptides can be produced using Applied Biosystems, Inc. Model 430A or 431A automatic peptide synthesizer (Foster City, Calif.) employing the chemistry provided by the manufacturer.

Also encompassed by the term SMDP and/or SCP are functional fragments or polypeptide analogs thereof. The term “functional fragment” refers to a peptide fragment that is a portion of a full length SMDP and/or SCP protein, provided that the portion has a biological activity, as defined above, that is characteristic of the corresponding full length protein. For example, a functional fragment of an invention SMDP and/or SCP protein can have the protein:protein binding activity prevalent in SMDPs and/or SCPs. In addition, the characteristic of a functional fragment of invention SMDP and/or SCP proteins to elicit an immune response is useful for obtaining an anti-SMDP and/or SCP antibodies. Thus, the invention also provides functional fragments of invention SMDP and/or SCP proteins, which can be identified using the binding and routine methods, such as bioassays described herein.

The term “polypeptide analog” includes any polypeptide having an amino acid residue sequence substantially the same as a sequence specifically shown herein in which one or more residues have been conservatively substituted with a functionally similar residue and which displays the ability to functionally mimic an SMDP and/or SCP as described herein. Examples of conservative substitutions include the substitution of one non-polar (hydrophobic) residue such as isoleucine, valine, leucine or methionine for another, the substitution of one polar (hydrophilic) residue for another such as between arginine and lysine, between glutamine and asparagine, between glycine and serine, the substitution of one basic residue such as lysine, arginine or histidine for another, or the substitution of one acidic residue, such as aspartic acid or glutamic acid for another.

The amino acid length of functional fragments or polypeptide anlogs of the present invention can range from about 5 amino acids up to the full-length protein sequence of an invention SMDP and/or SCP. In certain embodiments, the amino acid lengths include, for example, at least about 10 amino acids, at least about 20, at least about 30, at least about 40, at least about 50, at least about 75, at least about 100, at least about 150, at least about 200, at least about 250 or more amino acids in length up to the full-length SMDP and/or SCP protein sequence.

As used herein the phrase “conservative substitution” also includes the use of a chemically derivatized residue in place of a non-derivatized residue, provided that such polypeptide displays the required binding activity. The phrase “chemical derivative” refers to a subject polypeptide having one or more residues chemically derivatized by reaction of a functional side group. Such derivatized molecules include, for example, those molecules in which free amino groups have been derivatized to form amine hydrochlorides, p-toluene sulfonyl groups, carbobenzoxy groups, t-butyloxycarbonyl groups, chloroacetyl groups or formyl groups. Free carboxyl groups may be derivatized to form salts, methyl and ethyl esters or other types of esters or hydrazides. Free hydroxyl groups may be derivatized to form O-acyl or O-alkyl derivatives. The imidazole nitrogen of histidine may be derivatized to form N-im-benzylhistidine. Also included as chemical derivatives are those peptides which contain one or more naturally occurring amino acid derivatives of the twenty standard amino acids. For examples: 4-hydroxyproline may be substituted for proline; 5-hydroxylysine may be substituted for lysine; 3-methylhistidine may be substituted for histidine; homoserine may be substituted for serine; and ornithine may be substituted for lysine. Polypeptides of the present invention also include any polypeptide having one or more additions and/or deletions of residues, relative to the sequence of a polypeptide whose sequence is shown herein, so long as the required activity is maintained.

The present invention also provides compositions containing an acceptable carrier and any of an isolated, purified SMDP and/or SCP mature protein or functional polypeptide fragments thereof, alone or in combination with each other. These polypeptides or proteins can be recombinantly derived, chemically synthesized or purified from native sources. As used herein, the term “acceptable carrier” encompasses any of the standard pharmaceutical carriers, such as phosphate buffered saline solution, water and emulsions such as an oil/water or water/oil emulsion, and various types of wetting agents. The SMDP and/or SCP compositions described herein can be used, for example, in methods described hereinafter.

Also provided are antisense-nucleic acids having a sequence capable of binding specifically with full-length or any portion of an mRNA that encodes SMDP and/or SCP polypeptides so as to prevent translation of the mRNA. The antisense-nucleic acid may have a sequence capable of binding specifically with any portion of the sequence of the cDNA encoding SMDP and/or SCP polypeptides. As used herein, the phrase “binding specifically” encompasses the ability of a nucleic acid sequence to recognize a complementary nucleic acid sequence and to form double-helical segments therewith via the formation of hydrogen bonds between the complementary base pairs. An example of an antisense-nucleic acid is an antisense-nucleic acid comprising chemical analogs of nucleotides.

Compositions comprising an amount of the antisense-nucleic acid, described above, effective to reduce expression of SMDP and/or SCP polypeptides by passing through a cell membrane and binding specifically with mRNA encoding SMDP and/or SCP polypeptides so as to prevent translation and an acceptable hydrophobic carrier capable of passing through a cell membrane are also provided herein. Suitable hydrophobic carriers are described, for example, in U.S. Pat. Nos. 5,334,761; 4,889,953; 4,897,355, and the like. The acceptable hydrophobic carrier capable of passing through cell membranes may also comprise a structure which binds to a receptor specific for a selected cell type and is thereby taken up by cells of the selected cell type. The structure may be part of a protein known to bind to a cell-type specific receptor.

Antisense-nucleic acid compositions are useful to inhibit translation of mRNA encoding invention polypeptides. Synthetic oligonucleotides, or other antisense chemical structures are designed to bind to mRNA encoding SMDP and/or SCP polypeptides and inhibit translation of mRNA and are useful as compositions to inhibit expression of SMDP and/or SCP associated genes in a tissue sample or in a subject.

In accordance with another embodiment of the invention, kits are provided for detecting mutations, duplications, deletions, rearrangements and aneuploidies in SMDP and/or SCP genes comprising at least one invention probe or antisense nucleotide.

The present invention provides means to modulate levels of expression of SMDP and/or SCP polypeptides by employing synthetic antisense-nucleic acid compositions (hereinafter SANC) which inhibit translation of mRNA encoding these polypeptides. Synthetic oligonucleotides, or other antisense-nucleic acid chemical structures designed to recognize and selectively bind to mRNA, are constructed to be complementary to full-length or portions of an SMDP and/or SCP coding strand, including nucleotide sequences set forth in SEQ ID NOs:1, 3, 5, 7, 9, 11 and 13. The SANC is designed to be stable in the blood stream for administration to a subject by injection, or in laboratory cell culture conditions. The SANC is designed to be capable of passing through the cell membrane in order to enter the cytoplasm of the cell by virtue of physical and chemical properties of the SANC which render it capable of passing through cell membranes, for example, by designing small, hydrophobic SANC chemical structures, or by virtue of specific transport systems in the cell which recognize and transport the SANC into the cell. In addition, the SANC can be designed for administration only to certain selected cell populations by targeting the SANC to be recognized by specific cellular uptake mechanisms which bind and take up the SANC only within select cell populations. In a particular embodiment the SANC is an antisense oligonucleotide.

For example, the SANC may be designed to bind to a receptor found only in a certain cell type, as discussed supra. The SANC is also designed to recognize and selectively bind to target mRNA sequence, which may correspond to a sequence contained within the sequences shown in SEQ ID NOs:1, 3, 5, 7, 9, 11 and 13. The SANC is designed to inactivate target mRNA sequence by either binding thereto and inducing degradation of the mRNA by, for example, RNase I digestion, or inhibiting translation of mRNA target sequence by interfering with the binding of translation-regulating factors or ribosomes, or inclusion of other chemical structures, such as ribozyme sequences or reactive chemical groups which either degrade or chemically modify the target mRNA. SANCs have been shown to be capable of such properties when directed against mRNA targets (see Cohen et al., TIPS, 10:435 (1989) and Weintraub, Sci. American, January (1990), pp. 40; both incorporated herein by reference).

In accordance with yet another embodiment of the present invention, there is provided a method for the recombinant production of invention SMDPs and/or SCPs by expressing the above-described nucleic acid sequences in suitable host cells. Recombinant DNA expression systems that are suitable to produce SMDPs and/or SCPs described herein are well-known in the art. For example, the above-described nucleotide sequences can be incorporated into vectors for further manipulation. As used herein, vector (or plasmid) refers to discrete elements that are used to introduce heterologous DNA into cells for either expression or replication thereof.

Suitable expression vectors are well-known in the art, and include vectors capable of expressing DNA operatively linked to a regulatory sequence, such as a promoter region that is capable of regulating expression of such DNA. Thus, an expression vector refers to a recombinant DNA or RNA construct, such as a plasmid, a phage, recombinant virus or other vector that, upon introduction into an appropriate host cell, results in expression of the inserted DNA. Appropriate expression vectors are well known to those of skill in the art and include those that are replicable in eukaryotic cells and/or prokaryotic cells and those that remain episomal or those which integrate into the host cell genome.

As used herein, a promoter region refers to a segment of DNA that controls transcription of DNA to which it is operatively linked. Promoters, depending upon the nature of the regulation, may be constitutive or regulated. Exemplary promoters contemplated for use in the practice of the present invention include the SV40 early promoter, the cytomegalovirus (CMV) promoter, the mouse mammary tumor virus (MMTV) steroid-inducible promoter, Moloney murine leukemia virus (MMLV) promoter, and the like.

As used herein, expression refers to the process by which polynucleic acids are transcribed into mRNA and translated into peptides, polypeptides, or proteins. If the polynucleic acid is derived from genomic DNA, expression may, if an appropriate eukaryotic host cell or organism is selected, include splicing of the mRNA.

Prokaryotic transformation vectors are well-known in the art and include pBlueskript and phage Lambda ZAP vectors (Stratagene, La Jolla, Calif.), and the like. Other suitable vectors and promoters are disclosed in detail in U.S. Pat. No. 4,798,885, issued Jan. 17, 1989, the disclosure of which is incorporated herein by reference in its entirety.

Other suitable vectors for transformation of E. coli cells include the pET expression vectors (Novagen, see U.S. Pat. No. 4,952,496), e.g., pET11a, which contains the T7 promoter, T7 terminator, the inducible E. coli lac operator, and the lac repressor gene; and pET 12a-c, which contain the T7 promoter, T7 terminator, and the E. coli ompT secretion signal. Another suitable vector is the pIN-IIIompA2 (see Duffaud et al., Meth. in Enzymology, 153:492-507, 1987), which contains the 1 pp promoter, the lacUV5 promoter operator, the ompA secretion signal, and the lac repressor gene.

Exemplary, eukaryotic transformation vectors, include the cloned bovine papilloma virus genome, the cloned genomes of the murine retroviruses, and eukaryotic cassettes, such as the pSV-2 gpt system [described by Mulligan and Berg, Nature Vol. 277:108-114 (1979)] the Okayama-Berg cloning system [Mol. Cell Biol. Vol. 2:161-170 (1982)], and the expression cloning vector described by Genetics Institute [Science Vol. 228:810-815 (1985)], are available which provide substantial assurance of at least some expression of the protein of interest in the transformed eukaryotic cell line.

In accordance with another embodiment of the present invention, there are provided “recombinant cells” containing the nucleic acid molecules (i.e., DNA or mRNA) of the present invention. Methods of transforming suitable host cells, preferably bacterial cells, and more preferably E. coli cells, as well as methods applicable for culturing said cells containing a gene encoding a heterologous protein, are generally known in the art. See, for example, Sambrook et al., Molecular Cloning: A Laboratory Manual (2 ed.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA (1989).

Exemplary methods of transformation include, e.g., transformation employing plasmids, viral, or bacterial phage vectors, transfection, electroporation, lipofection, and the like. The heterologous DNA can optionally include sequences which allow for its extrachromosomal maintenance, or said heterologous DNA can be caused to integrate into the genome of the host (as an alternative means to ensure stable maintenance in the host).

Host organisms contemplated for use in the practice of the present invention include those organisms in which recombinant production of heterologous proteins has been carried out. Examples of such host organisms include bacteria (e.g., E. coli), yeast (e.g., Saccharomyces cerevisiae, Candida tropicalis, Hansenula polymorpha and P. pastoris; see, e.g., U.S. Pat. Nos. 4,882,279, 4,837,148, 4,929,555 and 4,855,231), mammalian cells (e.g., HEK293, CHO and Ltk⁻ cells), insect cells, and the like. Presently preferred host organisms are bacteria. The most preferred bacteria is E. coli.

In one embodiment, nucleic acids encoding the invention SMDPs and/or SCPs can be delivered into mammalian cells, either in vivo or in vitro using suitable viral vectors well-known in the art. Suitable retroviral vectors, designed specifically for “gene therapy” methods, are described, for example, in WIPO publications WO 9205266 and WO 9214829, which provide a description of methods for efficiently introducing nucleic acids into human cells. In addition, where it is desirable to limit or reduce the in vivo expression of the invention SMDP and/or SCP, the introduction of the antisense strand of the invention nucleic acid is contemplated.

Viral based systems provide the advantage of being able to introduce relatively high levels of the heterologous nucleic acid into a variety of cells. Suitable viral vectors for introducing invention nucleic acid encoding an SMDP and/or SCP protein into mammalian cells (e.g., vascular tissue segments) are well known in the art. These viral vectors include, for example, Herpes simplex virus vectors (e.g., Geller et al., Science, 241:1667-1669 (1988)), Vaccinia virus vectors (e.g., Piccini et al., Meth. in Enzymology, 153:545-563 (1987); Cytomegalovirus vectors (Mocarski et al., in Viral Vectors, Y. Gluzman and S. H. Hughes, Eds., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1988, pp. 78-84), Moloney murine leukemia virus vectors (Danos et al., PNAS, USA, 85:6469 (1980)), adenovirus vectors (e.g., Logan et al., PNAS, USA, 81:3655-3659 (1984); Jones et al., Cell, 17:683-689 (1979); Berkner, Biotechniques, 6:616-626 (1988); Cotten et al., PNAS, USA, 89:6094-6098 (1992); Graham et al., Meth. Mol. Biol., 7:109-127 (1991)), adeno-associated virus vectors, retrovirus vectors (see, e.g., U.S. Pat. Nos. 4,405,712 and 4,650,764), and the like. Especially preferred viral vectors are the adenovirus and retroviral vectors.

For example, in one embodiment of the present invention, adenovirus-transferrin/polylysine-DNA (TfAdpl-DNA) vector complexes (Wagner et al., PNAS, USA, 89:6099-6103 (1992); Curiel et al., Hum. Gene Ther., 3:147-154 (1992); Gao et al., Hum. Gene Ther., 4:14-24 (1993)) are employed to transduce mammalian cells with heterologous SMDP and/or SCP nucleic acid. Any of the plasmid expression vectors described herein may be employed in a TfAdpl-DNA complex.

As used herein, “retroviral vector” refers to the well-known gene transfer plasmids that have an expression cassette encoding an heterologous gene residing between two retroviral LTRs. Retroviral vectors typically contain appropriate packaging signals that enable the retroviral vector, or RNA transcribed using the retroviral vector as a template, to be packaged into a viral virion in an appropriate packaging cell line (see, e.g., U.S. Pat. No. 4,650,764).

Suitable retroviral vectors for use herein are described, for example, in U.S. Pat. No. 5,252,479, and in WIPO publications WO 92/07573, WO 90/06997, WO 89/05345, WO 92/05266 and WO 92/14829, incorporated herein by reference, which provide a description of methods for efficiently introducing nucleic acids into human cells using such retroviral vectors. Other retroviral vectors include, for example, the mouse mammary tumor virus vectors (e.g., Shackleford et al., PNAS, USA, 85:9655-9659 (1988)), and the like.

In accordance with yet another embodiment of the present invention, there are provided anti-SMDP and/or SCP antibodies having specific reactivity with an SMDP and/or SCP polypeptides of the present invention. Active fragments of antibodies are encompassed within the definition of “antibody”. Invention antibodies can be produced by methods known in the art using invention polypeptides, proteins or portions thereof as antigens. For example, polyclonal and monoclonal antibodies can be produced by methods well known in the art, as described, for example, in Harlow and Lane, Antibodies: A Laboratory Manual (Cold Spring Harbor Laboratory (1988)), which is incorporated herein by reference. Invention polypeptides can be used as immunogens in generating such antibodies. Alternatively, synthetic peptides can be prepared (using commercially available synthesizers) and used as immunogens. Amino acid sequences can be analyzed by methods well known in the art to determine whether they encode hydrophobic or hydrophilic domains of the corresponding polypeptide. Altered antibodies such as chimeric, humanized, CDR-grafted or bifunctional antibodies can also be produced by methods well known in the art. Such antibodies can also be produced by hybridoma, chemical synthesis or recombinant methods described, for example, in Sambrook et al., supra., and Harlow and Lane, supra. Both anti-peptide and anti-fusion protein antibodies can be used. (see, for example, Bahouth et al., Trends Pharmacol. Sci. 12:338 (1991); Ausubel et al., Current Protocols in Molecular Biology (John Wiley and Sons, NY (1989) which are incorporated herein by reference).

Antibody so produced can be used, inter alia, in diagnostic methods and systems to detect the level of SMDP and/or SCP present in a mammalian, preferably human, body sample, such as tissue or vascular fluid. Such antibodies can also be used for the immunoaffinity or affinity chromatography purification of the invention SMDP and/or SCP. In addition, methods are contemplated herein for detecting the presence of an invention SMDP and/or SCP protein in a tissue or cell, comprising contacting the cell with an antibody that specifically binds to SMDP and/or SCP polypeptides, under conditions permitting binding of the antibody to the SMDP and/or SCP polypeptides, detecting the presence of the antibody bound to the SMDP and/or SCP polypeptide, and thereby detecting the presence of invention polypeptides. With respect to the detection of such polypeptides, the antibodies can be used for in vitro diagnostic or in vivo imaging methods.

Immunological procedures useful for in vitro detection of target SMDP and/or SCP polypeptides in a sample include immunoassays that employ a detectable antibody. Such immunoassays include, for example, ELISA, Pandex microfluorimetric assay, agglutination assays, flow cytometry, serum diagnostic assays and immunohistochemical staining procedures which are well known in the art. An antibody can be made detectable by various means well known in the art. For example, a detectable marker can be directly or indirectly attached to the antibody. Useful markers include, for example, radionucleotides, enzymes, fluorogens, chromogens and chemiluminescent labels.

Invention anti-SMDP and/or SCP antibodies are contemplated for use herein to modulate the activity of the SMDP and/or SCP polypeptide in living animals, in humans, or in biological tissues or fluids isolated therefrom. The term “modulate” refers to a compound's ability to increase (e.g., via an agonist) or inhibit (e.g., via an antagonist) the biological activity of an invention SMDP and/or SCP protein, such as the participation in Siah-Mediated-Degradation via an SFC complex and the 26S proteosome. Accordingly, compositions comprising a carrier and an amount of an antibody having specificity for SMDP and/or SCP polypeptides effective to inhibit naturally occurring ligands or other SMDP and/or SCP-binding proteins from binding to invention SMDP and/or SCP polypeptides are contemplated herein. For example, a monoclonal antibody directed to an epitope of an invention SMDP and/or SCP polypeptide including an amino acid sequence set forth in SEQ ID NOs:2, 4, 6, 8, 10, 12 or 14, can be useful for this purpose.

The present invention further provides transgenic non-human mammals that are capable of expressing exogenous nucleic acids encoding SMDP and/or SCP polypeptides. As employed herein, the phrase “exogenous nucleic acid” refers to nucleic acid sequence which is not native to the host, or which is present in the host in other than its native environment (e.g., as part of a genetically engineered DNA construct). In addition to naturally occurring levels of SMDP and/or SCP, invention SMDPs and/or SCPs can either be overexpressed or underexpressed (such as in the well-known knock-out transgenics) in transgenic mammals.

Also provided are transgenic non-human mammals capable of expressing nucleic acids encoding SMDP and/or SCP polypeptides so mutated as to be incapable of normal activity, i.e., do not express native SMDP and/or SCP. The present invention also provides transgenic non-human mammals having a genome comprising antisense nucleic acids complementary to nucleic acids encoding SMDP and/or SCP polypeptides, placed so as to be transcribed into antisense mRNA complementary to mRNA encoding SMDP and/or SCP polypeptides, which hybridizes to the mRNA and, thereby, reduces the translation thereof. The nucleic acid may additionally comprise an inducible promoter and/or tissue specific regulatory elements, so that expression can be induced, or restricted to specific cell types. Examples of nucleic acids are DNA or cDNA having a coding sequence substantially the same as the coding sequence shown in SEQ ID NOs:1, 3, 5, 7, 9, 11 and 13. An example of a non-human transgenic mammal is a transgenic mouse. Examples of tissue specificity-determining elements are the metallothionein promoter and the L7 promoter.

Animal model systems which elucidate the physiological and behavioral roles of SMDP and/or SCP polypeptides are also provided, and are produced by creating transgenic animals in which the expression of the SMDP and/or SCP polypeptide is altered using a variety of techniques. Examples of such techniques include the insertion of normal or mutant versions of nucleic acids encoding an SMDP and/or SCP polypeptide by microinjection, retroviral infection or other means well known to those skilled in the art, into appropriate fertilized embryos to produce a transgenic animal. (See, for example, Hogan et al., Manipulating the Mouse Embryo: A Laboratory Manual (Cold Spring Harbor Laboratory, (1986)).

Also contemplated herein, is the use of homologous recombination of mutant or normal versions of SMDP and/or SCP genes with the native gene locus in transgenic animals, to alter the regulation of expression or the structure of SMDP and/or SCP polypeptides (see, Capecchi et al., Science 244:1288 (1989); Zimmer et al., Nature 338:150 (1989); which are incorporated herein by reference). Homologous recombination techniques are well known in the art. Homologous recombination replaces the native (endogenous) gene with a recombinant or mutated gene to produce an animal that cannot express native (endogenous) protein but can express, for example, a mutated protein which results in altered expression of SMDP and/or SCP polypeptides.

In contrast to homologous recombination, microinjection adds genes to the host genome, without removing host genes. Microinjection can produce a transgenic animal that is capable of expressing both endogenous and exogenous SMDP and/or SCP. Inducible promoters can be linked to the coding region of nucleic acids to provide a means to regulate expression of the transgene. Tissue specific regulatory elements can be linked to the coding region to permit tissue-specific expression of the transgene. Transgenic animal model systems are useful for in vivo screening of compounds for identification of specific ligands, i.e., agonists and antagonists, which activate or inhibit SMDP and/or SCP protein responses.

SMDP and/or SCP proteins, such as Siah-1, are contemplated herein to be a tumor suppressor proteins. Tumor suppressor proteins generally are thought to have a function in signal transduction. Mutation results in loss of function whereupon a signal pathway that the suppressor protein regulates is left in the “on” position, which results in unregulated cell proliferation resulting in cancerous tumor formation. Nearly all tumor suppressors regulate cell division, and proliferation, and may have involvement in biochemical pathways of development and the cell cycle.

The functions of the invention SMDP and/or SCP proteins support the role of both Siah and the invention SMDPs and/or SCPs in cellular pathways that affect protein degradation, such as by activating or inhibiting protein degradation, cell division and proliferation. Accordingly, invention SMDP and/or SCP proteins provide targets for treating a broad variety of pathologies, such as proliferative diseases, cancer pathologies, and the like.

For example, in accordance with yet another embodiment of the present invention, Siah-1 has been found to bind to the protein APC (Kinzler, et al., 1996, supra). The APC protein is known to bind to β-catenin and target it for ubiquitination and degradation (Korinek, V. et al., 1997, Science, 275:1784-1786, Rubinfeld, B. et al., 1997, Science, 275:1790-1792, and Morin, P. J. et al., 1997, Science, 275:1787-1790). Defects in the regulation of the APC/β-catenin pathway for cell growth control have been implicated in a variety of cancer pathologies, such as epithelial cancers, and the like. Thus, in accordance with the present invention Siah-1, and antagonist or agonists thereof, are contemplated for use in methods for treating a variety of cancers, such as epithelial cancer and the like, preferably by modulating β-catenin degradation. When used for binding to APC, fragments comprising the carboxy terminus of Siah-1, preferably comprising at least amino acids 252-298 of SEQ ID NO:2, are employed (See FIG. 3).

Invention nucleic acids, oligonucleotides (including antisense), vectors containing same, transformed host cells, polypeptides and combinations thereof, as well as antibodies of the present invention, can be used to screen compounds in vitro to determine whether a compound functions as a potential agonist or antagonist to invention polypeptides. These in vitro screening assays provide information regarding the function and activity of invention polypeptides, which can lead to the identification and design of compounds that are capable of specific interaction with one or more types of invention proteins or fragments thereof.

Thus, in accordance with yet another embodiment of the present invention, there are provided methods for identifying compounds which bind to, and preferably, modulate the activity of SMDP and/or SCP polypeptides. The invention proteins may be employed in a competitive binding assay. Such an assay can accommodate the rapid screening of a large number of compounds to determine which compounds, if any, are capable of binding to SMDPs and/or SCPs. Subsequently, more detailed assays can be carried out with those compounds found to bind, to further determine whether such compounds act as modulators, agonists or antagonists of invention SMDP and/or SCP proteins. Compounds that bind to and/or modulate invention SMDPs and/or SCPs can be used to treat a variety of pathologies mediated by invention SMDPs and/or SCPs, as described herein.

In accordance with another embodiment of the present invention, transformed host cells that recombinantly express invention polypeptides can be contacted with a test compound, and the modulating effect(s) thereof can then be evaluated by comparing the SMDP-mediated response (e.g., the degradation of a known Siah-mediated target, such as DCC or β-catenin) in the presence and absence of test compound, or by comparing the response of test cells or control cells (i.e., cells that do not express SMDP and/or SCP polypeptides), to the presence of the compound.

As used herein, a compound or a signal that “modulates the activity” of invention polypeptides refers to a compound or a signal that alters the activity of SMDP and/or SCP polypeptides so that the activity of the invention polypeptide is different in the presence of the compound or signal than in the absence of the compound or signal. In particular, such compounds or signals include agonists and antagonists. An agonist encompasses a compound or a signal that activates SMDP and/or SCP protein expression. Alternatively, an antagonist includes a compound or signal that interferes with SMDP and/or SCP expression. Typically, the effect of an antagonist is observed as a blocking of agonist-induced protein activation. Antagonists include competitive and non-competitive antagonists. A competitive antagonist (or competitive blocker) interacts with or near the site specific for agonist binding. A non-competitive antagonist or blocker inactivates the function of the polypeptide by interacting with a site other than the agonist interaction site.

As understood by those of skill in the art, assay methods for identifying compounds that modulate SMDP and/or SCP activity generally require comparison to a control. For example, one type of a “control” is a cell or culture that is treated substantially the same as the test cell or test culture exposed to the compound, with the distinction that the “control” cell or culture is not exposed to the compound. Another type of “control” cell or culture may be a cell or culture that is identical to the transfected cells, with the exception that the “control” cell or culture do not express native proteins. Accordingly, the response of the transfected cell to compound is compared to the response (or lack thereof) of the “control” cell or culture to the same compound under the same reaction conditions.

Accordingly, in accordance with another embodiment of the present invention, there is provided a bioassay for evaluating whether test compounds are capable of acting as agonists or antagonists for SMDP and/or SCP proteins, wherein said bioassay comprises: (a) culturing cells containing: DNA which expresses an SMDP and/or SCP or functional fragments thereof, wherein said culturing is carried out in the presence of at least one compound whose ability to modulate an activity of an SMDP and/or SCP is sought to be determined, wherein said activity is selected from a protein:protein binding activity or a protein degradation activity and thereafter (b) monitoring said cells for either an increase or decrease in the level of protein:protein binding or protein degradation.

Methods well-known in the art for measuring protein:protein binding or protein degradation can be employed in bioassays described herein to identify agonists and antagonists of SMDP and/or SCP proteins. For example, the Siah-1 over-expression assay described in Example 14 can be used to evaluate the cell degradation activity of recombinant SMDP and/or SCP proteins or mutants and/or analogs thereof, expressed in mammalian host cells.

As used herein, “ability to modulate protein degradation activity of an SMDP and/or SCP” protein refers to a compound that has the ability to either induce (agonist) or inhibit (antagonist) the protein degradation activity of SMDP and/or SCP proteins within a cell. Host cells contemplated for use in the bioassay(s) of the present invention include human and other mammalian cells (readily available from American Type Culture Collection), as well as genetically engineered yeast or bacteria that express human SMDPs and/or SCPs, and the like.

In yet another embodiment of the present invention, there are provided methods for modulating the protein degradation activity mediated by SMDP and/or SCP protein(s), said method comprising:

contacting an SMDP and/or SCP protein with an effective, modulating amount of an agonist or antagonist identified by the above-described bioassays.

Also provided herein are methods of treating pathologies, said method comprising administering an effective amount of an invention therapeutic composition. Such compositions are typically administered in a physiologically compatible composition.

Exemplary diseases related to abnormal cell proliferation contemplated herein for treatment according to the present invention include cancer pathologies, keratin hyperplasia, neoplasia, keloid, benign prothetic hypertrophy, inflammatory hyperplasia, and the like. Exemplary cancer pathologies contemplated herein for treatment include, gliomas, carcinomas, sarcomas, melanomas, hamartomas, leukemias, lymphomas, and the like.

Also contemplated herein, are therapeutic methods using invention pharmaceutical compositions for the treatment of pathological disorders in which there is too little cell division, such as, for example, bone marrow aplasias, immunodeficiencies due to a decreased number of lymphocytes, and the like. Methods of treating a variety of inflammatory diseases with invention therapeutic compositions are also contemplated herein, such as treatment of sepsis, fibrosis (e.g., scarring), arthritis, graft versus host disease, and the like.

Accordingly, the present invention contemplates therapeutic compositions useful for practicing the therapeutic methods described herein. Therapeutic compositions of the present invention, such as pharmaceutical compositions, contain a physiologically compatible carrier together with an invention SMDP and/or SCP (or functional fragment thereof), a SMDP and/or SCP modulating agent, such as a compound (agonist or antagonist) identified by the methods described herein, or an anti-SMDP and/or SCP antibody, as described herein, dissolved or dispersed therein as an active ingredient. In a preferred embodiment, the therapeutic composition is not immunogenic when administered to a mammal or human patient for therapeutic purposes.

As used herein, the terms “pharmaceutically acceptable”, “physiologically compatible” and grammatical variations thereof, as they refer to compositions, carriers, diluents and reagents, are used interchangeably and represent that the materials are capable of administration to a mammal without the production of undesirable physiological effects such as nausea, dizziness, gastric upset, and the like.

The preparation of a pharmacological composition that contains active ingredients dissolved or dispersed therein is well known in the art. Typically such compositions are prepared as injectables either as liquid solutions or suspensions; however, solid forms suitable for solution, or suspension, in liquid prior to use can also be prepared. The preparation can also be emulsified.

The active ingredient can be mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient in amounts suitable for use in the therapeutic methods described herein. Suitable excipients are, for example, water, saline, dextrose, glycerol, ethanol, or the like, as well as combinations of any two or more thereof. In addition, if desired, the composition can contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, and the like, which enhance the effectiveness of the active ingredient.

The therapeutic composition of the present invention can include pharmaceutically acceptable salts of the components therein. Pharmaceutically acceptable nontoxic salts include the acid addition salts (formed with the free amino groups of the polypeptide) that are formed with inorganic acids such as, for example, hydrochloric acid, hydrobromic acid, perchloric acid, nitric acid, thiocyanic acid, sulfuric acid, phosphoric acid, acetic acid, propionic acid, glycolic acid, lactic acid, pyruvic acid, oxalic acid, malonic acid, succinic acid, maleic acid, fumaric acid, anthranilic acid, cinnamic acid, naphthalene sulfonic acid, sulfanilic acid, and the like.

Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium hydroxide, ammonium hydroxide, potassium hydroxide, and the like; and organic bases such as mono-, di-, and tri-alkyl and -aryl amines (e.g., triethylamine, diisopropyl amine, methyl amine, dimethyl amine, and the like) and optionally substituted ethanolamines (e.g., ethanolamine, diethanolamine, and the like).

Physiologically tolerable carriers are well known in the art. Exemplary liquid carriers are sterile aqueous solutions that contain no materials in addition to the active ingredients and water, or contain a buffer such as sodium phosphate at physiological pH, physiological saline or both, such as phosphate-buffered saline. Still further, aqueous carriers can contain more than one buffer salt, as well as salts such as sodium and potassium chlorides, dextrose, polyethylene glycol and other solutes.

Liquid compositions can also contain liquid phases in addition to and to the exclusion of water. Exemplary additional liquid phases include glycerin, vegetable oils such as cottonseed oil, and water-oil emulsions.

As described herein, an “effective amount” is a predetermined amount calculated to achieve the desired therapeutic effect, e.g., to modulate the protein degradation activity of an invention SMDP and/or SCP protein. The required dosage will vary with the particular treatment and with the duration of desired treatment; however, it is anticipated that dosages between about 10 micrograms and about 1 milligram per kilogram of body weight per day will be used for therapeutic treatment. It may be particularly advantageous to administer such compounds in depot or long-lasting form as discussed hereinafter. A therapeutically effective amount is typically an amount of an SMDP and/or SCP-modulating agent or compound identified herein that, when administered in a physiologically acceptable composition, is sufficient to achieve a plasma concentration of from about 0.1 μg/ml to about 100 μg/ml, preferably from about 1.0 μg/ml to about 50 μg/ml, more preferably at least about 2 μg/ml and usually 5 to 10 μg/ml. Therapeutic invention anti-SMDP and/or SCP antibodies can be administered in proportionately appropriate amounts in accordance with known practices in this art.

Also provided are systems using invention SMDPs and/or SCPs, or functional fragments thereof, for targeting any desired protein for ubiquitination and degradation, thus enabling novel gene discovery through functional genomics strategies or providing the basis for ablating target proteins involved in diseases for therapeutic purposes.

In accordance with another embodiment of the invention, there are provided methods for “inducing the degradation of the function” of a desired protein from a particular cell or cell-system. As used herein the phrase “inducing the degradation of the function” refers to deleting, altering, modifying and/or degrading a target protein so that it no longer has the ability to perform its native physiological function. This method is useful to determine the physiological/cellular function of the degraded protein. Thus, this invention method is useful in alleviating one of the rate limiting steps in functional genomics.

The invention methods take advantage of the invention SMDP and/or SCP proteins or other protein-degradation binding domains provided herein to create a system that targets specific proteins for degradation by recruiting them to a SCF complex for ubiquitination and subsequent degradation by an appropriate proteosome, such as 26S proteosome. First, a protein or peptide fragment is selected that binds the protein targeted for degradation in a cell, which is referred to herein as the “target-protein binding domain.” Such protein or peptide fragment could be, for example: a domain of any known protein that interacts with the target protein; the Fab region of an anti-target-protein antibody (e.g., sFv, and the like); or a peptide aptamer obtained by screening (using, for example, yeast two-hybridization, phage display, or other screening methods) a random library of peptide aptamers. The target-protein binding domain is then fused (by engineering cDNAs in expression plasmids to form a chimera) with an appropriate protein-degradation binding domain selected from an invention SMDP and/or SCP, such as Siah, SIP, SAF-1, SAF-2 or SAD, and the like; or other known proteins involved in protein degradation, such as F-box containing proteins, (e.g., Skp1, and the like), SOCS-box containing proteins (see, e.g., Kamura et al., 1998, Genes Dev, 12:3872; and Starr and Hilton, 1999, Bioessays, 21:47), HECT family proteins (see, e.g., Huibregtse et al. 1995 Proc. Natl. Acad. Sci. USA 92:2563-2567), or any other subunit of an E3 ubiquitin ligase complex, and the like (see, e.g., Tyers and Williams, 1999, Science, 284:601-604; incorporated herein by reference in its entirety).

Similarly, with respect to ubiquitin-independent protein degradation involving ornithine decarboxylase (ODC), a “target-protein binding domain” is a protein or peptide fragment that binds the protein targeted for degradation in a cell. When fused with an appropriate protein-degradation binding domain of ODC, the target-protein binding domain binds the target protein, and degradation of the target protein is induced.

As used herein, the phrase “protein-degradation binding domain” refers to a protein region that functions to recruit the target protein into a member of the superfamily of E3 ubiquitin ligase complexes, such as the SCF complex, or to Siah-family proteins which may target some proteins for degradation independently of SCF complexes, where the protein-degradation binding domain and/or the target protein become ubiquitinated and then degraded, such as by the 26S proteosome, lysosomes and/or vacuoles (see, e.g., Tyers and Williams, 1999, Science, 284:601-604; and Ciechanover, 1998, supra). Exemplary protein-degradation domains can be obtained from a protein member of the ubiquitin-mediated protein-degradation family, for example, SIP, Siah, E7, Fwb7, UB1, Ub4, S5a, antizyme, and others, as disclosed herein and well known to those skilled in the art. As used herein, the phrase “a protein member of the ubiquitin-mediated protein-degradation family” refers to one of the numerous proteins that are known to interact, via protein:protein binding, in the ubiquitin system of intracellular protein degradation (see, e.g., Ciechanover et al., 1998, supra; and Tyers and Williams, supra, and the like).

Similarly, with respect to ubiquitin-independent protein degradation involving ODC, a “protein-degradation binding domain” is a protein region of ODC that functions to recruit the target protein for degradation by the 26S proteasome. As discussed below, a full-length ODC sequence or a functional fragment of ODC, e.g., an ODC C-terminus, functions as a “protein-degradation binding domain.”

In yet another embodiment contemplated by the present invention, methods are provided of identifying a nucleic acid molecules encoding a chimeric protein that modulates a cellular phenotype, said method comprising: (a) expressing, in a cell, a chimeric nucleic acid comprising a member of a nucleic acid library fused to nucleic acid encoding a protein degradation binding domain of a protein member of the ubiquitin-mediated protein degradation family; and (b) screening said cells for a modulation of said phenotype.

For example, unbiased nucleic acid libraries can be constructed wherein, each member of the nucleic acid library is expressed as an encoded protein fused to a particular protein-degradation binding domain, such as invention SMDPs and/or SCPs, e.g., Siah-1, SIP (see, e.g., Example 15), SAF-1, SAF-2, or SAD; or other known proteins involved in protein degradation, such as Skp1, F-box containing proteins, HECT family proteins, or any other subunit of an E3 ubiquitin ligase complex, and the like. As used herein a “nucleic acid library” comprises cDNA libraries, YAC libraries, BAC libraries, cosmid libraries, or any other source of nucleic acid encoding polypeptides. The chimeric nucleic acid encoding these fusion proteins is then introduced into cells possessing a particular phenotype to be assayed.

The cells are then subjected to a “screening” step which comprises selecting one or more cells in which the desired phenotype has been modulated (e.g., suppressed or enhanced). The phenotypes to be screened may be any chemical or physical representation of a cellular process, including but not limited to: cell proliferation in either an attached or detached (i.e., anchorage-independent) state, cell survival, cell death, cell secretion, cell migration, abnormal cell morphology, chemical reactivity (e.g., heavy metals, antibiotics, etc.), physical reactivity (e.g., heat, light, radiation, etc.), and the like.

Next, cDNAs are identified and isolated whose expression products function to modulate the desired phenotype within cells. The cDNAs identified by the invention method encode an invention chimeric protein that interacts, preferably by direct binding, with another protein in the cells that is targeted for degradation, thereby eliminating its physiological function. Accordingly, any target-protein that has one or more protein-binding or protein-interacting partners, or which homodimerizes/homo-oligomerizes is contemplated for degradation in the invention methods. The cDNA identified by the above-described method can be used to perform a two-hybrid screen, as described herein, to identify the protein-binding region of the partner to the target protein, or directly sequenced to determine the identity of the target protein if homo-dimerization or homo-oligomerization situation occurs.

Accordingly, also provided in accordance with the present invention are chimeric proteins, and encoding nucleic acids, comprising a target-protein binding domain operatively linked to a protein-degradation binding domain of a protein member of the ubiquitin-mediated protein-degradation family, or to a protein-degradation binding domain of ODC.

Exemplary proteins whose function can be targeted for degradation according to the invention methods, include any protein encoded by a known gene or cDNA whose function is desired. Exemplary targets include, for example, apoptosis-related proteins, cell-cycle regulatory proteins, heat shock proteins, transcription factors, or any other target protein which, when degraded, will modulate the phenotype of a cell.

Also provided are methods for treating a disease by degrading the function of a target protein, comprising introducing, into a cell, a chimeric protein comprising a target-protein binding domain operatively linked to a protein-degradation binding domain of a protein member of the ubiquitin-mediated protein-degradation family, or to a protein-degradation binding domain of ODC. For example, for a variety of proteins which, when expressed in overabundant or mutated form (e.g., an oncoprotein such as ras, or a genetic mutation, such as in the CF gene (cystic fibrosis gene) result in a known pathology, the chimeric protein of the invention may be used to therapeutically treat the disease, by way of reducing or completely eliminating, via protein degradation, the pathology causing protein. This treatment comprises fusion of a protein domain which binds the target pathology causing protein (i.e., the protein which causes the illness) with a particular protein-degradation binding domain as described herein. This chimeric protein may then be delivered to the location of the protein which causes the illness by intravenous therapy or gene therapy employing the methods described herein, or any other method well-known to one skilled in the art for delivering a protein to its binding target. As used herein, “treatment of a disease” refers to a reduction in the effects of the disease, including reducing the symptoms of the disease.

In accordance with another embodiment of the present invention, there are provided methods for diagnosing cancer, said method comprising detecting, in said subject, a defective sequence or mutant of SEQ ID NOs:1, 3, 5, 7, 9, 11 and 13.

In accordance with another embodiment of the present invention, there are provided diagnostic systems, preferably in kit form, comprising at least one invention nucleic acid in a suitable packaging material. The diagnostic nucleic acids are derived from the SMDP and/or SCP-encoding nucleic acids described herein. In one embodiment, for example, the diagnostic nucleic acids are derived from any of SEQ ID NOs:1, 3, 5, 7, 9, 11 and 13. Invention diagnostic systems are useful for assaying for the presence or absence of nucleic acid encoding SMDP and/or SCP in either genomic DNA or in transcribed nucleic acid (such as mRNA or cDNA) encoding SMDP and/or SCP.

A suitable diagnostic system includes at least one invention nucleic acid, preferably two or more invention nucleic acids, as a separately packaged chemical reagent(s) in an amount sufficient for at least one assay. Instructions for use of the packaged reagent are also typically included. Those of skill in the art can readily incorporate invention nucleic probes and/or primers into kit form in combination with appropriate buffers and solutions for the practice of the invention methods as described herein.

As employed herein, the phrase “packaging material” refers to one or more physical structures used to house the contents of the kit, such as invention nucleic acid probes or primers, and the like. The packaging material is constructed by well known methods, preferably to provide a sterile, contaminant-free environment. The packaging material has a label which indicates that the invention nucleic acids can be used for detecting a particular sequence encoding SMDP and/or SCP including the nucleotide sequences set forth in SEQ ID NOs:1, 3, 5, 7, 9, 11 and 13 or mutations or deletions therein, thereby diagnosing the presence of, or a predisposition for, cancer. In addition, the packaging material contains instructions indicating how the materials within the kit are employed both to detect a particular sequence and diagnose the presence of, or a predisposition for, cancer.

The packaging materials employed herein in relation to diagnostic systems are those customarily utilized in nucleic acid-based diagnostic systems. As used herein, the term “package” refers to a solid matrix or material such as glass, plastic, paper, foil, and the like, capable of holding within fixed limits an isolated nucleic acid, oligonucleotide, or primer of the present invention. Thus, for example, a package can be a glass vial used to contain milligram quantities of a contemplated nucleic acid, oligonucleotide or primer, or it can be a microtiter plate well to which microgram quantities of a contemplated nucleic acid probe have been operatively affixed.

“Instructions for use” typically include a tangible expression describing the reagent concentration or at least one assay method parameter, such as the relative amounts of reagent and sample to be admixed, maintenance time periods for reagent/sample admixtures, temperature, buffer conditions, and the like.

Ornithine Decarboxylase-Mediated Protein Degradation by a Ubiquitin-Independent Mechanism

Also provided are compositions and methods for targeting the destruction of selected polypeptides in eukaryotic cells based on the ubiquitin-independent mechanism by which ornithine decarboxylase (ODC) is degraded by the 26S proteasome. Expressing whole polypeptides, polypeptide domains, or peptide ligands fused to the carboxy (C) terminus of ODC promotes proteasome-dependent degradation of these chimeric fusion polypeptides and their interacting cellular target polypeptides. In some cases, the degradation of the interacting (targeted) polypeptide depends on co-expression of antizyme (AZ), providing an inducible switch for triggering the degradation process. The ODC/AZ system is useful for ablating expression of specific endogenous polypeptides and creates the expected lesions in cellular pathways that require these polypeptides. Thus this approach provides an additional tool for revealing the cellular phenotypes of gene products and for therapeutics based on destruction of targeted polypeptides.

AZ binding to ODC induces exposure of the carboxy (C) terminus of ODC and accelerates its degradation by 50- to 100-fold. Normally, this polypeptide degradation pathway is induced in response to polyamines (e.g., spermine, spermidine, putresine, and known polyamine analogues), which trigger AZ production, thus providing a negative feedback loop for maintaining appropriate intracellular levels of these molecules (reviewed in Coffino, Nat. Rev. Mol. Cell Biol. 2:188-194, 2001). A number of polyamine analogs are known to those of ordinary skill in the art and may be used in the practice of the present invention.

As used herein, the terms “C terminus of ODC,” “ODC C terminus,” “C-terminal region of ODC” or “ODC C-terminal region” and similar terms are used interchangeably to refer to any ODC polypeptide or functional fragment thereof (or a polynucleotide that encodes such a polypeptide) that binds the 26S proteasome and has ODC activity. Thus, an ODC C terminus functions as a “protein-degradation binding domain” as defined herein, although the resulting protein degradation is not ubiquitin-mediated. The term “ODC activity” refers to the activity of a C terminus ODC in directing the degradation of a target polypeptide by the 26S proteasome when the C terminus of ODC is fused to a target-protein binding domain, such as a ligand of the target polypeptide, directly or indirectly through a linker separating the ligand and the C terminus of ODC. An ODC C terminus optionally also includes a region of the ODC polypeptide required for homodimerization. A C terminus of ODC includes a full-length ODC polypeptide or a fragment of a full-length ODC polypeptide. Wild-type, or native, ODC polypeptide-encoding polynucleotides and fragments thereof may be obtained from any eukaryotic source, including but not limited to human or other mammalian cells. Alternatively, modified (including one or more nucleotide sequence changes from a reference wild-type sequence, e.g., by known mutagenesis techniques) and synthetic (made with a desired sequence that is different from a wild-type sequence, e.g., using a DNA synthesizer) ODC C terminus polypeptides may be used in the practice of the invention.

As used herein, the term “antizyme” (AZ) includes a full-length AZ polypeptide or any fragment of AZ that has AZ activity (or a polynucleotide that encodes such a polypeptide). The term “AZ activity” refers to the activity of AZ in binding ODC and inducing exposure of the C terminus of ODC, thereby catalyzing, i.e., increasing the rate of, degradation of ODC by the 26S proteasome. A full-length antizyme polypeptide may be employed. Alternatively, a fragment of antizyme that catalyzes ODC degradation may be employed. Wild-type AZ polypeptide and fragments thereof may be obtained from any eukaryotic source, including but not limited to human AZ. Alternatively, modified (non-native) AZ polypeptides may be used in the practice of the invention.

As used herein, the term “linker” includes any polypeptide or peptide sequence that is included between a ligand sequence and an ODC C terminus sequence in a fusion polypeptide according to the present invention (or a polynucleotide that encodes such a polypeptide). Any linker polypeptide that permits degradation, or preferably increases degradation, of a target protein, may be used in the practice of the invention. Wild-type linker polypeptides or peptides may be obtained from any source. Alternatively, modified (non-native) or synthetic linker polypeptides may be used in the practice of the invention. A variety of flexible linker (FL) sequences that increase the efficiency of degradation of target polypeptides are disclosed in the Example below.

Therefore, according to one embodiment of the invention, a polypeptide is targeted for destruction in a eukaryotic cell by expression in the cell of a fusion polypeptide that comprises a target-protein binding domain and a protein-degradation binding domain of ODC, i.e., a C terminus of ODC.

One embodiment of the invention is directed to determining the function of a polypeptide of interest that is encoded by a recombinant expression vector according to the present invention. According to one embodiment of the invention, the fusion polypeptide includes a linker between the target-protein binding domain and the protein-degradation binding domain, i.e., the ODC C terminus. According to another embodiment of the invention, such a fusion polypeptide comprises, in sequence from its amino (N) terminus to its carboxy (C) terminus, the target-protein binding domain, the linker portion, and the protein-degradation binding domain. According to a further embodiment, the fusion polypeptide includes an epitope tag located anywhere in the fusion polypeptide that does not interfere with function of the fusion polypeptide, to allow verification of protein production by immunoblotting and/or confirmation of binding to cellular target proteins by co-immunoprecipitation assays. When introduced into a host cell, the target-protein binding domain interacts with (e.g., binds to) the targeted polypeptide of interest, and ODC binds to the 26S proteasome, leading to degradation of the fusion polypeptide and the target polypeptide by the 26S proteasome. The resulting degradation of the targeted polypeptide of interest is detected by detection of a reduction in intracellular levels of the polypeptide of interest or changes in one or more phenotypes associated with such a reduction in levels of the polypeptide.

Exemplary polypeptides that can be targeted for degradation according to the methods of the present invention include any polypeptide, including, but not limited to, polypeptides involved in apoptosis, regulation of the cell cycle, heat shock, transcription factors, etc.

According to one embodiment of the invention, an expression vector that encodes and expresses a chimeric fusion polypeptide of the present invention is introduced into eukaryotic (e.g., mammalian) cells in vitro. According to another embodiment of the invention, such an expression vector is introduced into a eukaryotic cell, such as a mammalian embryonic stem (ES) cell or a fertilized or unfertilized egg cell, and the cell with the introduced expression vector develops into an organism, each cell of which includes the introduced expression vector. According to another embodiment of the invention, such an expression vector is introduced into a cell of a eukaryotic organism in vivo. According to another embodiment of the invention, such an expression vector is introduced into cells of an organism (e.g., bone marrow cells or isolated stem cells) ex vivo, then the cells are introduced into the organism. Accordingly, the present invention provides compositions that comprise such polynucleotides, including pharmaceutical compositions comprising such polynucleotides and a pharmaceutically acceptable carrier.

In another embodiment of the invention, isolated chimeric fusion polypeptides according to the invention are administered to cells in which a polypeptide of interest is expressed. Upon uptake by the cells, the fusion polypeptide binds to the polypeptide of interest, targeting its degradation by the 26S proteasome and reducing levels of the polypeptide of interest in the cells. Accordingly, the present invention provides compositions that comprise such fusion polypeptides, such as pharmaceutical compositions comprising such fusion polypeptides and a pharmaceutically acceptable carrier.

In another embodiment of the invention, methods are provided of identifying a polynucleotide that modulates a phenotype of a cell. As used herein, the term “modulates” is used to refer to any increase or decrease in the magnitude of a phenotype, or the appearance or disappearance of a phenotype, or any other detectable change in a phenotype of a cell (or a tissue, organ, or organism comprising such a cell). Such methods comprise: (a) introducing into the cell an isolated polynucleotide comprising a expression control sequence and a protein-coding sequence, operably linked to the expression control sequence, that encodes a polypeptide that comprises a ligand sequence that binds to a cellular polypeptide that is not degraded by a 26S proteasome in a cell comprising the cellular polypeptide and a targeting sequence, wherein expression of the polynucleotide in the cell causes the cellular polypeptide to be degraded by the 26S proteasome; and (b) observing a modulation of phenotype of the cell. In such methods of identifying, or screening for, polynucleotides that modulate a phenotype of a cell, for example, unbiased polynucleotide libraries can be screened, including but not limited to cDNA, cosmid, yeast artificial chromosome (YAC), or bacterial artificial chromosome (BAC) libraries, or any other source of polynucleotides. The phenotype to be screened may be any chemical or physical representation of a cellular process, including but not limited to: proliferation in an attached or detached (i.e., anchorage dependent or independent) state, survival, death, secretion, migration, morphology, reactivity to chemical substances (e.g., to heavy metals, antibiotics, etc.) or physical stimuli (e.g., heat, light, radiation, etc.), and the like. A polynucleotide that causes a modulate in phenotype of a cell in such an assay can be used to perform a two-hybrid screen to determine the protein-binding region of the partner to the targeted protein or directly sequenced to determine the identity of the target protein if homo-dimerization or homo-oligomerization occurs.

Organisms useful for functional studies with recombinant polynucleotides according to the present invention are those in which the polynucleotide is able to inhibit expression of a target polypeptide in cells that express the target polypeptide. Organisms include an embryo, a juvenile stage, or an adult animal, including, but not limited to, a fish, a frog, a mouse, a rat, guinea pig, a sheep, a monkey, or a human. As used herein, the term “cell” refers to an isolated cell or cells in vitro, tissues, organs, or whole organisms.

Similarly, polynucleotides according to the present invention also are useful for generating model organisms for the study of diseases. Disease conditions associated with loss or reduction of function of a particular polypeptide in a higher organism such as a human can be generated in a model organism if the model organism has a homologous or orthologous polypeptide. For example, a polynucleotide according to the present invention that targets the homologue or orthologue in the model organism is introduced into the model organism (such as a mouse, for example), thereby creating a “knock out” of the homologue or orthologue. Reduction in expression of the homologue or orthologue present in the model organism results in a morphant organism that exhibits the disease condition or other detectable phenotype resulting from the loss or reduction in function of the homologous or orthologous polypeptide. Such morphants can be used to screen for compounds that are useful for treating the disease condition or alleviating the severity of the disease condition. To screen for compounds that are useful for treating a disease condition or alleviating the severity of the disease condition, morphants exhibiting the disease condition can be contacted with candidate compounds and then assessed to determine whether the disease condition is lessened.

Polynucleotides according to the present invention also can be used to identify the function of polypeptides not known to be associated with a disease condition. To identify polypeptides not known to be associated with a disease condition, a polynucleotide according to the present invention is introduced into a wild-type organisms and morphants exhibiting any particular disease condition or other detectable phenotype are chosen for further analysis. A collection of polynucleotides according to the present invention can be used to generate a collection of morphants that can, in turn, be used to identify drug targets as well as to develop novel treatments for a disease condition. A potential drug target, for example, is identified as the polypeptide whose reduction in expression led to the disease condition.

To identify polypeptides whose excessive activity leads to a disease condition, polynucleotides according to the present invention are introduced into organisms exhibiting the disease condition. Those organisms whose disease state is lessened by the polynucleotides are further examined to identify polynucleotides whose expressions have been reduced. These polynucleotides are identified as useful targets for the development of novel treatments for the particular disease.

Expression vectors according to the present invention also can be used therapeutically as treatments for disease conditions. In order to treat a disease condition associated with expression (or overexpression) of a particular polypeptide, an expression vector that expresses a chimeric fusion polypeptide according to the present invention is introduced into an organism in need of treatment by any known means, as discussed below. According to one embodiment of the invention, such an expression vector is introduced into a cell of a eukaryotic organism in vivo. According to another embodiment of the invention, such an expression vector is introduced into cells of an organism (e.g., bone marrow cells or isolated stem cells) ex vivo, then the cells are introduced into the organism. Upon introduction into cells and expression within the cells, a cellular polypeptide is targeted for destruction, providing a therapeutic benefit. For example, such targeted polypeptides may include polypeptides that, when inappropriately expressed (e.g., over- or underexpressed or expressed or expressed at an abnormal time or location) or expressed in a mutated form, cause a disease symptom in a patient, including oncoproteins (e.g., ras), cellular receptors, ion transporters or channels (e.g., the cystic fibrosis gene), etc.

All U.S. patents and all publications mentioned herein are incorporated in their entirety by reference thereto. The invention will now be described in greater detail by reference to the following non-limiting examples.

EXAMPLES

Unless otherwise stated, the present invention was performed using standard procedures, as described, for example in Maniatis et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA (1982); Sambrook et al., Molecular Cloning: A Laboratory Manual (2 ed), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA (1989); Davis et al., Basic Methods in Molecular Biology, Elsevier Science Publishing, Inc., New York, USA (1986); or Methods in Enzymology: Guide to Molecular Cloning Techniques Vol. 152, S. L. Berger and A. R. Kimmerl Eds., Academic Press Inc., San Diego, USA (1987)).

Library screening by the yeast two-hybrid method was performed herein as described (Durfee et al., 1993; Sato et al., 1995; Matsuzawa et al. 1998) using the pGilda plasmid encoding the desired amino acid region as bait, an appropriate cDNA library, and the EGY48 strain S. cerevisiae (MATa, trp1, ura3, his, leu2::plexApo6-leu2). Cells were grown in either YPD medium with 1% yeast extract, 2% polypeptone, and 2% glucose, or in Burkholder's minimal medium (BMM) fortified with appropriate amino-acids as described previously (Sato et al., 1994). Transformations were performed by a LiCi method using 0.25 mg of pJG4-5-cDNA library DNA, and 5 mg of denatured salmon sperm carrier DNA. Clones that formed on Leu deficient BMM plates containing 2% galactose/1% raffinose were transferred to BMM plates containing leucine and 2% glucose, and filter assays were performed for β-galactosidase measurements as previously described.

Example 1 Yeast Two-Hybrid Screen of BAG-1 Binding Proteins to Obtain cDNA Encoding Siah-1α

The mouse BAG-1 amino acid sequence was cloned into the pGilda plasmid and used as bait to screen a human Jurkat T-cell cDNA library. From an initial screen of ˜1.6×10⁷ transformants, 298 clones were identified that trans-activated the LEU2 reporter gene based on ability to grow on leucine-deficient media. Of those, 30 colonies were also positive for β-galactosidase. These 30 candidate transformants were then cured of the LexA/BAG-1 bait plasmid by growth in media containing histidine and then mated with each of 5 different indicator strains of cells containing one of following LexA bait proteins: BAG-1 (1-219), Bax (1-171), v-Ras, Fas (191-335), or Lamin-C. The mating strain was RFY206 (MATa, his3D200, leu2-3, lys2D201, ura3-52, trp1D::hisG), which had been transformed with pGilda-BAG-1 or various control proteins and selected on histidine-deficient media. This resulted in 23 clones which displayed specific two-hybrid binding interactions with BAG-1. DNA sequencing analysis revealed 4 cDNAs encoding portions of Siah-1.

Example 2 Isolation of Full-Length Human Siah-1α cDNAs

To obtain the complete sequence of human Siah-1, cDNA fragments containing the 5′ end of human Siah 1 were PCR-amplified from Jurkat randomly primer cDNAs by using a forward primer 5′ GGGAATTCGGACTTATGGCATGTAAACA-3′ (SEQ ID NO:42) containing an EcoRI site and a reverse primer 5′ TAGCCAAGTTGCGAATGGA-3′ (SEQ ID NO:43), based on sequences of EST database clones (NCBI ID: AA054272, AA258606, AA923663, AA418482, and AI167464). The PCR products were digested with EcoRI and BamHI, then directly subcloned into the EcoRI and SalI sites of pcI plasmid into which the cDNA derived from pJG4-5-Siah (22-298) had previously been cloned, as a BamHI-XhoI fragment. The complete human Siah-1α (cDNA and amino acid sequence is set forth in SEQ ID Nos:1 and 2, respectively. The human Siah-1α sequence contains 16 N-terminal amino acids that are not present in the human Siah-1β protein.

Example 3 Yeast Two-Hybrid Screen of Siah-1 Binding Proteins to Obtain cDNA Encoding SIP-L and SIP-S

Human Siah-1α cDNA encoding amino acids 22-298 of SEQ ID NO:1 (corresponding to amino acids 6-282 set forth in Nemani et al., supra) was cloned into the pGilda plasmid and used as a bait to screen a human embryonic brain cDNA library (Invitrogen) in EGY48 strain S. cerevisiae. From an initial screen of 2.0×10⁷ transformants, 322 clones were identified that trans-activated the LEU2 reporter gene based on ability to grow on leucine-deficient media. Of those, 32 colonies were also positive for β-galactosidase. These 32 candidate transformants were then cured of the LexA/Siah-1 bait plasmid by growth in media containing histidine and then mated with each of 5 different indicator strains of cells containing one of following LexA bait proteins: Siah-1 (22-298), Bax (1-171), v-Ras, Fas (191-335), or BAG-1. The mating strain was RFY206 which had been transformed with pGilda-Siah-1 or various control proteins and selected on histidine-deficient media. This resulted in 11 clones which displayed specific two-hybrid interactions with Siah-1. DNA sequencing analysis revealed 5 cDNAs encoding portions of SIP-L, 1 cDNA encoding portions of SIP-S, 3 cDNAs encoding portions of APC(2681-2843), and 2 cDNAs encoding portions of Siah-1. The SIP-L and SIP-S clones were sequenced and the resulting nucleotide sequences are set forth in SEQ ID Nos:3 and 5, respectively.

Example 4 Yeast Two-Hybrid Screen of Skp1 Binding Proteins to Obtain cDNA Encoding SAF-1 and SAD

Human Skp1 cDNA encoding amino acids 91-163 of (Zhang et al., 1995, Cell, 82:915-925) was cloned into the pGilda plasmid as a bait to screen a human embryonic brain cDNA library (Invitrogen) in EGY48 strain S. cerevisiae. From an initial screen of ˜1.2×10⁸ transformants, 130 clones were identified that trans-activated the LEU2 reporter gene based on ability to grow on leucine-deficient media. Of those, 36 colonies were also positive for β-galactosidase. These 36 candidate transformants were then cured of the LexA/BAG-1 bait plasmid by growth in media containing histidine and then mated with each of 5 different indicator strains of cells containing one of following LexA bait proteins: Skp1 (91-163), SIP-L, Bax (1-171), v-Ras, Fas (191-335), or Siah-1. The mating strain was RFY206 which had been transformed with pGilda-Skp1 or various control proteins and selected on histidine-deficient media. This resulted in 3 clones which displayed specific two-hybrid interactions with Skp1 and 18 clones which displayed specific two-hybrid interactions with both Skp1 and SIP-L. DNA sequencing analysis revealed 12 cDNAs encoding portions of SAF-1 and 9 cDNAs encoding portions of SAD. The SAF-1 and SAD clones were sequenced and the resulting nucleotide sequences are set forth in SEQ ID Nos:7 (SAF-1α), 9 (SAF-1β), and 13 (SAD).

Example 5 Isolation of Full-Length SAF-2 cDNAs

Full-length cDNA encoding a human SAF-2 protein was PCR-amplified from ZAPII Jurkat cDNA library (Stratagene) by using a forward primer 5′-GTGAATTCATGCAACTTGTACCTGATATAGAGTTC-3′ (SEQ ID NO:44) containing an EcoRI site and a reverse primer 5′-GGACTCGAGGCTCTACAGAGGCC-3′ (SEQ ID NO:45), based on human DNA sequence from clone 341E18 on chromosome 6p11.2-12.3 (AL031178). The PCR products were digested with EcoRI and XhoI, then directly subcloned into the EcoRI and XhoI sites of the plasmid pcDNA3. The corresponding plasmid was sequenced and the results are set forth in SEQ ID Nos: 11 and 12.

Example 6 Yeast Two-Hybrid Screen of SIP-L Binding Proteins

The human SIP-L cDNA encoding full-length SIP-L was cloned into the pGilda plasmid as a bait to screen a human embryonic brain cDNA library (Invitrogen) in EGY48 strain S. cerevisiae. From an initial screen of 1.5×10⁷ transformants, 410 clones were identified that trans-activated the LEU2 reporter gene based on ability to grow on leucine-deficient media. Of those, 68 colonies were also positive for β-galactosidase. These 32 candidate transformants were then cured of the LexA/SIP-L bait plasmid by growth in media containing histidine and then mated with each of 32 different indicator strains of cells containing one of following LexA bait proteins: SIP-L, Bax (1-171), v-Ras, Fas (191-335), or BAG-1. The mating strain was RFY206 which had been transformed with pGilda-SIP-L or various control proteins and selected on histidine-deficient media. This resulted in 16 clones which displayed specific two-hybrid interactions with SIP-L. DNA sequencing analysis revealed 3 cDNAs encoding portions of Skp1, 1 cDNA encoding portions of Siah-1, and 11 cDNAs encoding portions of SIP-L. These results indicate that SIP-L binds to Skp1 and Siah-1 proteins, and is able to homodimerize with SIP isoforms.

Example 7 A Cell Proliferation Functional Assay of SIP/Siah Interaction

The effects of invention SIP-L and SIP-S proteins on Siah-1-induced cell cycle arrest in 293T epithelial cancer cells was examined and the results are shown in FIG. 4. Human embryonic kidney 293 cells were maintained in high-glucose DMEM medium containing 10% fetal calf serum, 1 mM L-glutamine, and antibiotics. Cells (˜5×10⁵) in 60 mm plates were transfected with a total of 3.0 μg of plasmid DNAs encoding Siah-1 alone or together with SIP or SIP-S by a calcium phosphate precipitation technique. After 24 hours, the cells were harvested and the number of viable and dead cells were counted using trypan blue dye exclusion assays. Efficiency of transient transfection was estimated by in situ β-galactosidase assay using a portion of the transfected cells. The transient transfection efficiency of the T293 cells was consistently 90%.

As revealed in FIG. 4, over-expression of Siah-1 resulted in decreased numbers of viable cells after 24 hours, without an increase in cell death. Thus, Siah-1 suppresses proliferation of 293 cells. Co-transfection of SIP-L with Siah-1 did not substantially alter Siah-1-mediated growth suppression. In contrast, the SIP-S protein abrogated the growth suppressive effects of Siah-1, which indicates that the invention SIP-S protein affects Siah-1 intracellularly in a different manner than SIP-L.

Example 8 In Vitro SIP:Siah-1 Protein Interaction Assays

Complementary cDNA encoding SIP-L was cloned into pGEX-4T-1 and expressed in XL-1-blue cells (Stratagene, Inc.), and affinity-purified using glutathione-Sepharose as is well-known in the art. Purified GST-fusion proteins (0.5-1.0 μg immobilized on 10-20 μl of glutathione beads) and 2.5 ul of rat reticulocyte lysates (TNT-Lysates; Promega, Inc.) containing ³⁵S-labeled in vitro translated (IVT) Siah-1 proteins were incubated in 0.1 ml of HKMEN (10 mM HEPES [pH7.2], 142 mM KCl, 5 mM MgCl₂, 2 mM EGTA, 0.1% NP-40) at 4° C. for 30 minutes. The beads were washed 3× with 1 ml HKMEN solution, followed by boiling in 25 μl of Laemmli-SDS sample buffer. The eluted proteins were analyzed by SDS-PAGE (12%) and detected by fluorography. Use of equivalent amounts of intact GST-fusion proteins and successful IVT of each protein was confirmed by SDS-PAGE analysis using Coomassie staining or autoradiography, respectively.

The results are shown in FIG. 5A and indicate that Siah-1 binds to SIP-L and homodimerizes in vitro.

Example 9 Co-Immunoprecipitation Assay of SIP:Siah-1

Two×10⁶ 293T cells in 100 mm plates were transiently transfected with 10 μg of pCDNA3-myc-SIP-L and 10 mg of pcDNA3-HA-Siah-1 (amino acids 97-298 of SEQ ID NO:2). Twenty-four hours later, cells were disrupted by sonication in 1 ml of HKMEN solution containing 0.2% NP-40, 0.1 μM PMSF, 5 μg/ml leupeptin, 1 μg/ml aprotinin, and 1 μg/ml pepstatin. After preclearing with normal mouse IgG and 10 ml protein A-agarose, immunoprecipitations were performed using 10 ml of anti-myc antibody-conjugated sepharose (Santa Cruz) to precipitate the myc-SIP-L fusion, or an anti-IgG as a control at 4° C. for 4 hours. After extensive washing in HKMEN solution, immune-complexes were analyzed by SDS-PAGE/immunoblotting using anti-HA antibody 12CA5 (Boehringer Mannheim), followed by HRPase-conjugated goat anti mouse immunoglobulin (Amersham, Inc.), and detected using an enhanced chemiluminescence (ECL) system (Amersham, Inc.).

The results are shown in FIG. 5B and indicate that SIP proteins bind to Siah-1 intracellularly.

Example 10 Yeast Two-Hybrid Assay of Siah-1:APC Binding Specificity

One μg of plasmids encoding fusion proteins of the LexA DNA-binding domain fused to Siah-1, APC(2681-284), BAG-1, Bax, Ras, Fas, FLICE were co-transformed into yeast strain EGY48 with 1 μg of pJG4-5 plasmid encoding fusion proteins of the B42 trans-activation domain fused to APC(2681-2843) and Siah-1. Transformed cells were grown on semi-solid media lacking leucine or containing leucine as a control which resulted in equivalent amounts of growth for all transformants. Plasmid combinations that resulted in growth on leucine-deficient media within 4 days were scored as positive (+). β-galactosidase activity of each colony was tested by filter assay and scored as blue (+) versus white (−) after 60 minutes.

The results are shown in Table 1, and indicate that APC interacts specifically by direct binding with Siah-1, and not with BAG-1, Bax, Ras, Fas nor FLICE. TABLE 1 Specific Interaction of Siah with SIP Lex A B42 Leu⁺ β-Gal⁺ Siah-1 APC (2681-2843) + + APC (2681-2843) Siah-1 + + BAG-1 APC (2681-2843) − − Bax APC (2681-2843) − − Ras APC (2681-2843) − − Fas APC (2681-2843) − − FLICE APC (2681-2843) − − empty APC (2681-2843) − −

Example 11 Yeast Two-Hybrid Assay of Siah-1:SIP Binding Specificity

One μg of plasmids encoding fusion proteins of the LexA DNA-binding domain fused to Siah-1, Siah-2, BAG-1, Bax, Ras, Fas, FLICE, and SIP-L were co-transformed into yeast strain EGY48 with 1 μg of pJG4-5 plasmid encoding fusion proteins of the B42 trans-activation domain fused to SIP-L, SIP-S, Siah-1, Siah-2, BAG-1, Bax, and Ras. Transformed cells were grown on semi-solid media lacking leucine or containing leucine as a control which resulted in equivalent amounts of growth for all transformants. Plasmid combinations that resulted in growth on leucine-deficient media within 4 days were scored as positive (+). β-galactosidase activity of each colony was tested by filter assay and scored as blue (+) versus white (−) after 60 minutes.

The results are shown in Table 2, and indicate that SIP proteins interact specifically by direct binding with Siah proteins. SIP-L was found to interact with Siah-1 and Siah-2, and not with BAG-1, Bax, Ras, Fas nor FLICE. SIP-S was also found to interact with Siah-1. Table 2 also reveals that the SIP-L homodimerization domain is within amino acids 73-228 of SIP-L (SEQ ID NO:4) TABLE 2 Specific Interaction of Siah with SIP Lex A B42 Leu⁺ β-Gal⁺ Siah-1 SIP-L + + Siah-1 SIP-S + + Siah-2 SIP-L + + BAG-1 SIP-L − − Bax SIP-L − − Ras SIP-L − − FLICE SIP-L − − empty SIP-L − − SIP-L Siah-1 + + SIP-L Siah-2 + + SIP-L BAG-1 − − SIP-L Bax − − SIP-L Ras − − SIP-L SIP-L + + SIP-L SIP-S − −

Example 12 Mapping of Siah-APC Interaction Domains

Expression plasmids encoding fusion proteins of Siah-1α fragments corresponding to: SEQ ID NO:2 amino acids 22-298; 22-251; 22-193; 97-298; and 46-102, fused to the B-42 trans-activation domain were co-transformed into yeast EGY48 cells with a plasmid encoding a chimeric fusion protein of the Lex A DNA-binding domain fused to amino acids 2681-2843 of APC “APC(2681-2843).” Transformed cells were grown on semi-solid media lacking leucine or containing leucine as a control. Plasmid combinations that resulted in growth on leucine-deficient media within 4 days were scored as positive (+). β-galactosidase activity for each colony was tested by filter assay and scored as blue (+) versus white (−) (β-gal) based on a 1 hour of color development.

The results are shown in FIG. 3 and indicate that a region within the 47 carboxy terminal amino acids of Siah-1α (SEQ ID NO:2) is required for binding to APC.

Example 13 Mapping of SKP-1, SIP-L, SAF-1, and SAD Interaction Domains

Expression plasmids encoding fusion proteins of SAF-1α and functional fragments thereof corresponding to SEQ ID NO:8 amino acids 68-443; 80-443; and 258-443, were fused to the B-42 trans-activation domain. Likewise, expression plasmids encoding fusion proteins of SAD and functional fragments thereof corresponding to SEQ ID NO:14 amino acids 128-447; and 360-447, were fused to the B-42 trans-activation domain. These SAF-1-fragment- and SAD-fragment-B-42 fusion proteins were co-transformed into yeast EGY48 cells with a plasmid encoding a chimeric fusion protein of the Lex A DNA-binding domain fused to either SKP1, SIP-L, SAF-1, or SAD. Transformed cells were grown on semi-solid media lacking leucine or containing leucine as a control. Plasmid combinations that resulted in growth on leucine-deficient media within 4 days were scored as positive (+). β-galactosidase activity for each colony was tested by filter assay and scored as blue (+) versus white (−) (β-gal) based on a 1 hour of color development.

The results are shown in FIGS. 6A and 6B. FIG. 6A indicates that SAF-1 interacts by direct binding to Skp1, SIP-L and SAD, but does not interact with Siah-1. A region within the SAF-1 fragment corresponding to amino acids 80-257 of SEQ ID NO:8 is required for SIP-L interaction, whereas a region within amino acids 258-443 of SAF-1 is required for Skp1 and SAD interaction.

FIG. 6B indicates that SAD interacts by direct binding to Skp1, SIP-L and SAF-1, but does not interact with Siah-1. A region within the SAD fragment corresponding to amino acids 1-127 of SEQ ID NO:14 is required for SAF-1 interaction; a region within amino acids 128-359 of SAD is required for Skp1 interaction; and a region within amino acids 360-447 of SEQ ID NO:14 is required for SIP-L interaction.

Example 14 Effect of Siah-1 Over-Expression on Stability of β-Catenin

293T cells were transiently transfected with a plasmid encoding myc-tagged β-catenin and either pcDNA3, pcDNA3-Siah-1, or pcDNA3-Siah-1 (97-298; amino acids 97-298 of SEQ ID NO:2). Whole cell lysates were prepared, normalized for total protein content (25 μg per lane) and analyzed by SDS-PAGE/immunoblotting using an anti-Myc tag antibody.

FIG. 7 indicates that expression of full-length Siah-1 abolishes, by degradation, the presence of β-catenin within cells, whereas expression of amino acids 97-298 of Siah-1 (SEQ ID NO:2) does not result in β-catenin degradation. Thus, a region within amino acids 1-96 of SEQ ID NO:2 (Siah-1α), which contains the N-terminal “Ring” domain, is required for protein degradation.

Example 15 Demonstration of SIP-Mediated Degradation of a Target Protein, TRAF6

An invention SIP-based method for targeted degradation of proteins was applied to the degradation TRAF proteins. The schematic in FIG. 9 shows the strategy employed for targeted degradation of specific TRAF-family proteins. A chimeric protein is expressed from the plasmid pcDNA3 in which SIP-L (SEQ ID NO:3) is fused with bacterial thioredoxin containing various TRAF-binding peptides displayed on the surface of thioredoxin, as described by Brent and colleagues (Colas, et al. Nature, 380: 548, 1996; Cohen, et al. Proc. Natl. Acad. Sci., 95: 14272, 1998; Geyer, et al. Proc. Natl. Acad. Sci., 96: 8562, 1999; Fabbrizio, et al. Oncogene, 18: 4357, 1999). The TRAF-binding peptide binds to a member of the TRAF-family, and targets the TRAF-protein for ubiquitination and subsequent proteosome-dependent degradation because the SIP-region of the chimeric protein recruits ubiquitin-conjugating enzymes (E2s) to the protein complex.

Isolation of target-protein binding domain peptides that selectively bind TRAF2 and TRAF6. A peptide aptamer library was screened by the yeast two-hybrid method to identify peptides that bind to either TRAF2 or TRAF6 using the methods described in Leo, et al. J Biol Chem, 274:22414, 1999. TRAFs are a family of signal transducing proteins involved in cytokine receptor signaling inside cells. The sequences of the resulting TRAF-binding peptides are set forth in (Tables 3 and 4). TABLE 3 Selected Traf 2 aptamer clones Clones (SEQ ID NO:) SLxCIxLR motif 219 (15) SESPGALRSGSLRCISLRIC 230 (16) VCRGRIRSGSLRCISLRICR 221 (17)   LLRLGCIRLLMLRRGVVFRL 208 (18)   VLFLSLRFWGLNIVVMGRLL 215 (19)    CRSLGVIVGGTEAAGAPTFI LS motif 208 (20)    VLFLSLRFWGLNIVVMGRLL 213 (21) WLRRGLVGVFFLLSRVMVGI 218 (22)    SLGLSVCIGRRAGGGFRGFG 237 (23)    RFALSIGVCVVVRVGICLGM LV motif 209 (24)  SAVLVLVYVSAALRGRGFGI 227 (25) HGGGRGALVSVMYLCGFIRL Non-Consensus motif 231 (26)  RGRVIGMWVGLRCRMFLV

TABLE 4 Selected Traf 6 Aptamer Clones Clones (SEQ ID NO:) WR motif 625 (27) VDWAVYSVVWRYTTT* 631 (28)  KTSVILVWRLSLFFCLYRSL* 606 (29)   ANRCWRE* 628 (30) EGTLSKRMWRTHN* 640 (31)    SWRDMTQSGM* 604 (32)   DVPWQRACARQ* 607 (33)  LERVARWVL* 602 (34)  VADVLVFWGYVF* DVxVF motif 602 (34) VADVLVFWGYVF* 613 (35) GDVGVFPE* Non-Consensus motif 603 (36) PEMMLEGPKYCLxLxE* 609 (37) LLYGALA* 612 (38) GAIKFAHESCE* 616 (39) PMAMD* 632 (40) QEEEM* 639 (41) ISVVHGIGSDSD* *Termination codon

SIP-fusion chimeric protein construction. An invention SIP-fusion chimeric construct is generated by combining the open reading frame (ORF) of SIPL, followed immediately by restriction enzyme sites allowing for subcloning of desired target-protein-binding domains (e.g. peptides or protein domains). These SIP-fusions are then transfected into mammalian cells to eliminate by protein degradation specific target proteins which bind the subcloned peptides/protein domains by recruiting them into the ubiquitin conjugating complex.

Engineering of the parent SIP-vector (SIPpcDNA3.1) cassette. Oligonucleotides corresponding to the 5′ and 3′end of SIP_(L) were used in PCR to amplify the entire ORF of SIP_(L) (SEQ ID NO:3). The forward primer contains a Hind III restriction site linker (5′-GATCAAGCTTATGGCTTCAGAAGAGCTACAG; (SEQ ID NO:46) restriction site is underlined) followed immediately by the SIP_(L) (SEQ ID NO:3) start codon; the reverse primer contains an EcoRI restriction site and mutations in the stop codon allowing for translational readthrough (5′-GATCGAATTCtccAAATTCCGTGTCTCCTTTGGCTTG; (SEQ ID NO:47) mutated stop codon is in lowercase). The generated PCR product was then agarose gel-purified and digested with Hind III and EcoRI restriction enzymes (New England BioLabs; Beverly, Mass.). The product was again gel-purified before ligating into Hind III/EcoRI digested pcDNA3.1 expression vector (Invitrogen; Carlsbad, Calif.) with T4-DNA ligase (New England BioLabs). This construct was termed SIPpcDNA3.1.

For the construction of SIP-thioredoxin (Trx) peptide-aptamer fusions, clones from a peptide-aptamer library screened against Traf6 (see Table 4) were amplified by PCR with the following primers: (SEQ ID NO:48) Forward: 5′-CCTCTGAATTCCATATGAGCGATAAAATTATTCACC (EcoRI underlined); (SEQ ID NO:49) Reverse: 5′-GATCCTCGAGTAGATGGCCAGCTAGGCCAGGTTA (Xho I underlined).

The resulting PCR products (˜350-370 bp) contain the ORF of thioredoxin (Trx) with the selected peptide aptamers inserted into its active-loop. The products were then digested with EcoRI and Xho I before ligating into the EcoRI/XhoI-digested SIPpcDNA3.1 cassette using T4-DNA ligase. Final clone constructs were numbered and were confirmed by sequencing before using in transfection studies.

Tranfection: HEK293T cells were transiently transfected by a lipofectamine method with various amounts (1 vs 4 μg) of pcDNA3 plasmids encoding either SIP-TR fusion protein lacking a TRAF6-binding peptide (“SIP”) or SIP-TR fusion protein displaying one of the peptides shown in Table 4 above (set forth in FIG. 10 as S603, S604, S606). In some cases, the proteosome inhibitor MG132 (10 μM) was added to cultures to prevent protein turnover. SIP* in FIG. 10 corresponds to the control expression product of parental construct SIP pcDNA3.1

To determine the efficacy of the SIP:TRAF-binding peptide chimeric proteins, levels of TRAF6 protein were then measured two days later by immunoblotting using a anti-TRAF6-specific antiserum (Santa Cruz Biotech, Inc.) in experiments where HEK293T cell lysates were normalized for total protein content (25 μg per lane). The cell lysates were analyzed by SDS-PAGE/immunoblotting using an enhanced chemiluminescence detection method, as described previously (Leo, et al. J Biol Chem, 274: 22414, 1999). The results shown in the left panel of FIG. 10 show that SIP-TR fusion proteins displaying TRAF6-binding peptides (S603, S604, and S613) induce a reduction in TRAF6 protein levels, with the S603 peptide representing the most potent of these.

To determine the specificity of the SIP:TRAF-binding peptide chimeric proteins, the same immunoblots were reprobed with an antiserum against SIP to demonstrate equivalent levels of production of SIP-TR fusion proteins, or with antibodies specific for TRAF2 to reveal selective degradation of TRAF6 but not TRAF2. The results shown in the right panel of FIG. 10 show that addition of a proteosome inhibitor, MG132, prevents the reductions in TRAF6. Note also that TRAF2 protein is not degraded, demonstrating the specificity of the targeting approach.

Example 16 Demonstration of Ornithine Decarboxylase-(ODC) Mediated Degradation of a Target Protein

The levels of intracellular proteins are regulated by proteasome-dependent proteolysis. The selective degradation of cellular proteins is mediated primarily by both the ubiquitin-dependent and -independent proteasome pathways. In this example, the substrate receptor of a major proteolytic machinery is engineered to direct the degradation of otherwise stable cellular proteins in mammalian cells.

Strategy for the selective degradation of cellular protein by chimeric ODC proteins and antizyme. Ornithine decarboxylase (ODC) is degraded in a 26S proteasome antizyme-dependent manner, which does not require ubiquitination. In order to target the protein of interest (Targets), the adapter protein or peptide, which binds to target protein, is covalently fused to ODC for the degradation of protein complex by the 26S proteasome. A model of antizyme-dependent targeted protein degradation by ODC-conjugated proteins is shown in FIG. 11A. FIG. 11B shows the amino acid sequence of the ODC-fusion protein (SEQ ID NO:50)(human ODC sequence GenBank M16650).

Targeted degradation of TRAF6 by ODC-TRAF6C and ODC-RANK peptide. For targeted degradation of TRAF6, HEK293T cells were transiently transfected with plasmid encoding HA-TRAF6 (0.5 μg), HA-TRAF2 (0.5 μg), ODC (0.5 μg), ODC-TRAF6C (0.5 μg), ODC-RANK peptide (0.5 μg) ODC-CD40CT (0.5 μg) or myc-Antizyme (0.5 μg) in various combinations, as indicated in FIG. 12 (total DNA amount normalized). After 24 h, cell lysates were prepared from duplicate dishes of transfectants, normalized for total protein content (20 μg per lane), and analyzed by SDS-PAGE. Immunoblotting was performed using antibodies specific for the tags HA (TRAF6) or Myc (ODC or Antizyme), with detection by enhanced chemiluminescence (ECL). Levels of TRAF6 mRNA were measured by Northern blot (mRNA).

Expression of ODC-TRAF6C in HEK293T cells induced marked reductions in HA-TRAF proteins, with or without co-expressing plasmids encoding antizyme. In contrast, expression of ODC-TRAF6-RANK peptide decreased TRAF6 proteins in an antizyme-dependent manner. Expression of ODC-CD40 did not reduce TRAF6 protein. Neither ODC-TRAF6C nor ODC-RANK peptide affected the expression of TRAF2 proteins. Moreover, reductions in TRAF6 protein levels were not due to a decrease in TRAF6 mRNA, as determined by northern blot. Therefore, the degradation of TRAF6 by ODC-TRAF6C was antizyme-independent but the degradation of TRAF6 by ODC-RANK peptide was antizyme-dependent.

Other examples for ODC-adapter-induced degradation of target protein(s). The activity of ODC-adapter-induced degradation of other target protein(s) was tested. Antizyme-dependent targeted degradation of retinoblastoma (Rb) by ODC-E7 peptide is shown in FIG. 13A. HEK293T cells were transiently transfected with plasmid encoding HA-Rb (0.5 μg), ODC (0.5 μg), ODC-E7 peptide (0.5 μg) or myc-Antizyme (0.5 μg) in various combinations, as indicated in FIG. 13A (total DNA amount normalized). Antizyme-independent targeted degradation of Cdk2 by ODC-p21 waf-1 is shown in FIG. 13B. HEK293T cells were transiently transfected with plasmid encoding myc-Cdk2 (0.5 μg), ODC (0.5 μg), ODC-p21waf-1 (0.5 μg) or myc-Antizyme (0.5 μg) in various combinations, as indicated in FIG. 13B (total DNA amount normalized). Antizyme-independent targeted degradation of IKKβ by ODC-IKKβ (leucine-zipper domain) is shown in FIG. 13C. HEK293T cells were transiently transfected with plasmid encoding HA-IKKβ (0.5 μg), ODC (0.5 μg), ODC-IKKβ-LZ (0.5 μg) or myc-Antizyme (0.5 μg) in various combinations, as indicated in FIG. 13C (total DNA amount normalized). After 24 h, cell lysates were prepared from duplicate dishes of transfectants, normalized for total protein content (20 μg per lane), and analyzed by SDS-PAGE. Immunoblotting was performed using antibodies specific for Rb, Cdk2, IKKβ or HSC70 (as a control), with ECL-based detection.

Analysis of interactions of ODC-TRAF6C and TRAF6. For analysis of interactions of ODC-TRAF6C and TRAF6, HEK293T cells were transiently transfected with plasmids encoding hemaglutinin (HA)-tagged TRAF6 and ODC (0.5 μg), ODC-TRAF6C peptide (0.5 μg) or antizyme (0.5 μg) in various combinations, as indicated in FIG. 14 (total DNA amount normalized). After 24 h, 10 μM MG132 was added into culture media, and the cells were incubated another 6 hours. Lysates were normalized for total protein content and subjected to immunoprecipitation using 20 μl of anti-myc monoclonal antibody-conjugated beads. After recovering immune-complexes with beads and washing, the immunoprecipitates were analyzed by SDS-PAGE. Immunoblotting was performed using an anti-HA monoclonal antibody, with ECL-based detection. As a control, 0.1 volume of input cell lysate was loaded directly in the same gel.

To preliminarily assess whether ODC-TRAF6 and antizyme can exist in a complex with TRAF6, the TRAF6 proteins were tested for co-immunoprecipitation with ODC-TRAF6C using monoclonal antibodies against the myc epitope tag. As shown in FIG. 14, TRAF6 was recovered in TRAF6C-ODC, but not control ODC-empty, immune-complexes prepared from cells expressing ODC-TRAF6C.

Targeted degradation of TRAF6 by ODC-RANK peptide is proteasome-dependent. To test whether targeted degradation of TRAF6 by ODC-RANK peptide is proteasome-dependent, HEK293T cells were transiently transfected with 0.2 μg plasmid encoding HA-TRAF6 (0.5 μg), ODC-RANK peptide (0.5 μg) or myc-Antizyme (0.5 μg) in various combinations, as indicated in FIG. 15 (total DNA amount normalized). After 24 h, cells were either untreated or treated with 1 μM MG132 (MG132), 1 nM Epoximycine (Epox.), 10 μM Lactastacine (Lact.) or 1 μM Trypsin inhibitor (Tryp.) for 6 hours. Cell lysates were prepared from duplicate dishes of transfectants, normalized for total protein content (20 μg per lane), and analyzed by SDS-PAGE. Immunoblotting was performed using antibodies specific for HA.

As shown in FIG. 15, degradation of TRAF6 by ODC-RANK peptide and antizyme was inhibited by proteasome inhibitors, MG132, Epoximycine and Lactastacine but not by trypsin inhibitor. These results indicate that the degradation is S26 proteasome dependent.

Pulse-chase analysis of TRAF6 turnover rate. Pulse-chase analysis of ectopically expressed HA-tagged TRAF6 was performed. HEK293T cells were transiently co-transfected with plasmids encoding HA-TRAF6 and ODC-RANK peptide, with or without myc-Antizyme. After 24 hours, cells were pulse-labeled with ³⁵S-methionine and cysteine, and then chased with media lacking the labeled amino acids. Cells were lysed at the indicated times (FIG. 16), and the expressed HA-TRAF6 was recovered by immunoprecipitation via a HA epitope tag. Immunoprecipitad HA-TRAF6 was subjected to SDS-PAGE, and dried gels were analyzed with a PhosphorImager. Data from pulse-chase analysis is presented as the average±SD from duplicate experiments (FIG. 16B; −antizyme, closed circles; +antizyme, open circles). The blots shown are representative of duplicate experiments (FIG. 16A).

The turnover rate of the TRAF6 was increased in the 293T cells transiently transfected with ODC-RANK peptide and antizyme, as compared to the cells tranfected with ODC-RANK peptide alone. These results demonstrate that ODC-RANK peptide and antizyme promote down-regulation of TRAF6 in a post-translational manner.

Functional analysis using ODC-E7 peptide. To assess whether ODC-E7 peptide reduces endogenous Rb protein level and affects its cellular function, HEK293T cells were transiently transfected with ODC-E7 peptide and antizyme. Degradation of endogenous Rb protein by ODC-E7 is shown in FIG. 17A. HEK293T cells (100 mm dish) were transiently transfected with 2 μg plasmid encoding ODC (2 μg), ODC-E7 peptide (2 μg) or myc-Antizyme (2 μg) in various combinations, as indicated in FIG. 17A (total DNA amount normalized). After 48 h, lysates were normalized for total protein content and subjected to immunoprecipitation using 1 μg of anti-Rb monoclonal antibody. After recovering immune-complexes with protein G and washing, the immunoprecipitates were analyzed by SDS-PAGE. Immunoblotting was performed using an anti-Rb monoclonal antibody with ECL-based detection.

The effect of ODC-E7 on E2F reporter activity was also tested. HEK293T cells were transiently transfected with a reporter gene plasmid (0.1 μg) that contains a E2F responsive element cloned upstream of a luciferase reporter gene, together with 0.01 μg of pCMVβ-gal as a transfection-efficiency control, and 0.1 μg of the indicated plasmids encoding ODC, ODC-E7 or Antizyme in various combinations, as indicated in FIG. 17B (bars correspond to plasmid combinations as indicated in FIG. 17A)(total DNA amount normalized). Luciferase activity was measured in cell lysates 24 hr later and normalized relative to β-galactosidase (mean±std. dev.; n=3).

As shown in FIG. 17A, endogenous Rb protein was degraded by ODC-E7 peptide with antizyme. Since transcription factor E2F activity is normally suppressed by Rb in proliferating cells, the effects of ODC-E7 and antizyme on E2F activity was explored using transient transfection reporter gene assays. Expression of ODC-E7 plus antizyme induced a >5-fold increase in E2F transcriptional activity in HEK293T cell lines (FIG. 17B). In contrast, ODC-empty plus antizyme or ODC-E7 alone failed to activate E2F transcription activity. Therefore, ODC-E7 peptide affects endogenous Rb protein levels and E2F activity.

Effect of ODC-RANK peptide and ODC-TRAF6C on IL-1-induced NFκB reporter activity. Previous data have suggested that TRAF6 may play an important role in IL-1-mediated NFκB activation but not in TNFα-mediated NFκB activation. Therefore, the effects of ODC-TRAF6C and ODC-RANK peptide on both IL-1- and TNFα-induced NFκB activation were examined.

To test the effect of ODC-RANK peptide and ODC-TRAF6C on IL-1-induced NFκB reporter activity, HEK293T cells were transiently transfected with a reporter gene plasmid (0.1 μg) that contains a NFκB responsive element cloned upstream of a luciferase reporter gene, together with 0.01 μg of pCMVβ-gal as a transfection-efficiency control, and 0.1 μg of plasmids encoding ODC, ODC-TRAF6C, ODC-RANK peptide, or Antizyme in various combinations, as indicated in FIG. 18 (total DNA amount normalized). After 24 hours, cells were treated with 50 ng/ml IL-1 or 10 ng/ml TNFα for an additional 24 hours. Luciferase activity was measured in cell lysates and normalized relative to β-galactosidase (mean±std. dev.; n=3).

As shown in FIG. 18, expression of ODC-TRAF6C or ODC-RANK peptide in HEK293T cells induced marked reductions in NFκB reporter activity. In contrast, ODC-TRAF6C and ODC-RANK peptide did not affect the TNFα-madiated NFκB activation. These results confirm that TRAF6 is an important mediator in IL-1-induced signal transduction by using conditional inactivation of TRAF6 proteins.

A summary of the activity of various protein-degradation binding domains fused with ligands (target-protein binding domains) in the degradation of particular targets is shown in Table 5.

Example 17 Targeting Protein Destruction by Using a Ubiquitin-Independent, Proteasome-Mediated Degradation Pathway

Plasmids. The cDNAs encoding human AZ (70-228) and human ODC (full-length) were PCR-amplified from either human placenta or human fetal brain randomly primed cDNA libraries (Stratagene). To create the C-terminal fusion cassette vectors, cDNAs encoding ODC (full-length), Siah-interacting protein (SIP) (full-length), Siah1 (full-length), monoubiquitin (full-length), and S5a (full-length) were PCR-amplified with a forward primer containing BglII site on the 5′ end and a reverse primer containing EcoRI site on the 3′ end and subcloned into the BamHI and EcoRI sites of pcDNA3 plasmid (Invitrogen) with an N-terminal Myc epitope-tag (MEQKLISEEDL) and flexible linkers (FLs) consisting of either the Bcl-2 loop (residues 31 to 94), GGS, or AGGGSGGGGSGGGGSGGGGS. To create amino-terminal fusion cassette vectors, cDNAs encoding E7 (31-105) and Fbx7 (full-length) were PCR-amplified with a forward primer containing a XhoI site on the 5′ end and a reverse primer containing ApaI site on the 3′ end and subcloned into the XhoI and ApaI sites of the pcDNA3-myc vector. Ubiquitin mutant (G76V) was generated by two-step PCR-based mutagenesis using a full-length human monoubiquitin cDNA. Adaptors, TRAF6 (271-530), TRAF2 (Δ RING), E7 (2-34), p21^(waf-)1 (full-length), Caspase-9 (1-92), Apaf-1 (1-87), FADD (1-78), IKKα (304-758), IKK^(β) (305-745), and BAG-1 (full-length), were PCR-amplified and subcloned into each of the cassette vectors. To create the luciferase reporter plasmid containing an E2F binding site, primers 5′-CTGCAATTTCGCGCCAAACTTGTGCAATTTCGCGCCAAACTTGC-3′ and 5′-TCGAGCAAGTTTGGCGCGAAATTGCACAAGTTTGGC GCGAAATTGCACTCGA-3′ were annealed and ligated into pGL3E vector cleaved with Sac and HindIII (Krek et al., Science 262:1557-1560, 1993). The reporter gene plasmid containing four tandem HIV-NFκB response elements has been described in Galang et al., Oncogene 9:2913-2921, 1994.

Transfections and Cell Culture. HEK293T cells were maintained in high-glucose DMEM containing 10% FCS, 1 mM _(L)-glutamine, and antibiotics. Cells (approximately 5×10⁵) in six-well plates were transfected with plasmid DNAs by using Lipofectamine 2000 (Invitrogen). In some cases, 50 μg/ml cycloheximide was added to prevent polypeptide synthesis.

Immunoblots. Cells were lysed in 1 ml of HKMEN solution containing 0.5% Nonidet P-40, 0.1 μM PMSF, 5 μg/ml leupeptin, 1 μg/ml aprotinin, 1 μg/ml pepstatin, and 20 μM MG132. Lysates were analyzed by SDS/PAGE/immunoblotting using various antibodies, followed by HRPase-conjugated goat anti-mouse or anti-rabbit Ig (Amersham Pharmacia) and detected by using enhanced chemiluminescence (Amersham Pharmacia).

Pulse-Chase Analysis. For pulse-chase analysis of ectopically expressed HA-tagged TRAF6 (271-530) or IKK^(β) (305-745), HEK239T cells were transiently transfected in six-well plates. After 24 h, cells were pulse-labeled for 1 h with 0.1 mCi (1 Ci=37 GBq) of [³⁵S]methionine and [³⁵S]cysteine per well and then chased with cold media. Cells were lysed in RIPA buffer (0.05 M Tris.HCl, pH 7.2/0.15 M NaCl/1% Triton X-100/1% deoxycholate/0.1% SDS) supplemented with protease inhibitors. After preclearing with 20 μl of protein G-Sepharose for 1 h at 4° C., HA-TRAF6 or HA-IKK^(β) were immunoprecipitated by using rat anti-HA monoclonal antibody (3F10, Invitrogen) adsorbed to protein G-Sepharose beads at 4° C. for 4 h. After three washes with RIPA buffer, immunoprecipitates were subjected to SDS/PAGE. Dried gels were analyzed with a PhosphorImager (Molecular Dynamics).

Reporter Gene Assays. NFκB and E2F transcriptional activity were measured in HEK293T cells by transient transfection reporter gene assays. Cells at approximately 50% confluence in 24-well plates were cotransfected with 0.1 μg of reporter plasmids containing NFκB- or E2F-binding sites cloned upstream of a luciferase gene, 0.01 μg of pCMVβ-LacZ control plasmid, and 0.1 μg of various additional plasmids, as indicated. After 24 h, cells were lysed, and the relative amount of luciferase activity was measured according to the manufacturer's instructions (Promega), normalizing all values relative to beta-galactosidase activity.

Results

To explore technologies for inducing proteasome-dependent degradation of target polypeptides, we engineered plasmids to express in mammalian cells various chimeric polypeptides in which a polypeptide involved in ubiquitination mechanisms was fused to polypeptides or protein domains known to interact with specific target polypeptides. A protein-interaction domain (adapter) is expressed with ODC attached to its C terminus with a flexible linker (FL) sequence AGGGS(GGGGS)₃. ODC is known to form homodimers. The ODC-adapter fusion binds target polypeptides and docks on the 26S proteasome. AZ catalyzes degradation of the ODC-adapter polypeptide by the proteasome along with the interacting target polypeptide.

Twelve pairs of interacting polypeptides were studied, chosen randomly from reagents available in our laboratory, including: (i) the C-terminal TRAF domain (residues 271-530) of the adapter protein TRAF6, which binds TRAF6 (Ishida et al., J. Biol. Chem. 271:28745-28748, 1996), (ii) a peptide (residues 341-349) from the cytosolic domain of the TNF receptor (TNFR)-family protein RANK, known to bind TRAF6 (Ye et al., Nature 418:443-447, 2002); (iii) the cytosolic domain of TNFR-family member CD40, known to bind TRAF2 (Rothe et al., Science 269:32767-32770, 1995), (iv) I-TRAF, a TRAF2-binding protein (Rothe et al., Proc. Natl. Acad. Sci. USA 93:8241-8246, 1996); (v and vi) the leucine zipper of IKK^(β), which binds IKKα and IKK^(β) (Woronicz et al., Science 278:866-869, 1997); (vii) a peptide from papillomavirus E7 protein, which binds Rb; (viii) the CARD domain of proCaspase-9, which binds Apaf1; (ix) The CARD domain of Apaf-1, which binds proCaspase-9 (Zhou et al., Proc. Natl. Acad. Sci. USA 96:11265-11270, 1999); (x) the DED domain of adapter protein FADD, which binds proCaspase-8; (xi) BAG1, a Hsp70-binding cochaperone (Takayama et al., EMBO J. 16:4887-4896, 1997), and (xii) p21^(Waf-1), a Cdk2 inhibitor (Harper et al., Cell 75, 805-816, 1993). Protein or peptide ligands were expressed in HEK293T cells as fusion polypeptides with an N- or C-terminus-appended protein known to participate in protein-ubiquitination reactions, including (i) SIP, a protein known to bind the E3 ligase Siah1 and the Skp1 protein of Skp1/cullin/F-box protein complexes (Matsuzawa and Reed, Mol. Cell 7:915-926, 2001); (ii) Siah-1, a RING-domain containing E3 ligase (Matsuzawa et al., EMBO J. 17:2736-2747, 1998); (iii) E7, a papillomavirus protein with reported E3 ligase activity (Boyer et al., Cancer Res. 56:4620-4624, 1996; Jones et al., Virology 258:406-414, 1999); (iv) a fragment of the F-box protein Fbx7, in which the substrate-binding domain was substituted, leaving the Skp1-binding region; (v) ubiquitin G76V, a nonhydrolyzable variant of ubiquitin previously used to confer proteasome-sensitivity on polypeptides; (vi) a tandem 4′ oligomer of ubiquitin G76V (Stack et al., Nat. Biotechnol. 18:1298-1302, 2000); and (vii) S5a, a subunit of the proteasome involved in substrate recognition (Deveraux et al., J. Biol. Chem. 270:23726-23729, 1995). In most cases, the protein ligand was separated from the ubiquitin-pathway domain by a FL consisting of the sequence AGGGS(GGGGS)₃ (Hoedemaeker et al., J. Biol. Chem. 272:29784-29789, 1997). All constructs included an epitope tag, allowing verification of polypeptide production by immunoblotting and confirmation of binding to cellular target polypeptides by co-immunoprecipitation assays.

The ability of these fusion polypeptides to induce reductions in the steady-state levels of endogenous and plasmid-expressed interacting proteins was then explored by immunoblot analysis of HEK293T cells transfected to high efficiency (>90%) with plasmids encoding the fusion polypeptides. The target polypeptides were coexpressed with epitope tags by cotransfection by using a plasmid with a strong constitutive promoter (CMV immediate-early region promoter) to ensure continuous production of target polypeptides and avoid artifactual reductions that might be caused by unanticipated effects of the chimeric fusion polypeptides on pathways that affect endogenous gene expression and to avoid false-negatives due to nontransfected cells. Although not every possible combination was tested (Table 6), none of these fusion polypeptides successfully reduced levels of target polypeptides, based on 40 combinations tested. TABLE 6 Ligand Target ODC (N) ODC + Az SIP (N) Siah (N) E7 (C) Fbx7 (C) Ub1 (N) Ub4 (N) S5a (N) TRFAF6-C TRAF6 ↓ ↓ — — — — — — — RANK-pep. TRAF6 — ↓ — — — — — — — CD40CT TRAF2 — — nd nd nd nd nd nd — I-TRAF TRAF2 — — — nd nd nd nd nd — IKKα(LZ) IKKα — — — nd nd nd nd nd — IKKβ(LZ) IKKβ ↓ ↓ — nd nd nd nd nd — E7 Rb — ↓ — — nd — — — — Caspase9(CARD) Apaf1 — — — — — — — — nd Apaf1(CARD) Caspase9 nd — — — — — — — nd FADD(DED) Caspase8 nd — — — — — — — nd BAG-1 HSP70 — — nd nd nd nd nd nd nd p21 Cdk2 ↓ ↓ nd — — nd nd nd nd Success Ratio All Targets 5/12 0/9 0/7 0/6 0/6 0/6 0/6 0/7

Testing of an AZ-Based System for Targeted Polypeptide Degradation. Given the lack of efficacy of fusion polypeptides based on known components of the ubiquitination machinery to effectively induce degradation of interacting polypeptides, we turn to an alternative strategy based on knowledge of the mechanism by which ODC is degraded by the proteasome through ubiquitin-independent mechanisms. For this purpose, protein ligands were expressed as fusion polypeptides with ODC at their C termini, thus exposing the C terminus of ODC, which is known to bind the proteasome independently of ubiquitin.

An FL sequence was also inserted between the protein ligands and ODC. Three types of linkers were tested, including a 63-aa segment from the Bcl-2 protein (residues 31-94), which is known from structural studies to constitute a nonstructured, flexible peptide rich in prolines and glycines (Chang et al., EMBO J. 16:968-977, 1997), a Gly-Gly-Pro tripeptide, and the sequence [Gly-Gly-Gly-Gly-Ser]₃. These ODC fusion polypeptides were then expressed in HEK293T cells alone or in combination with AZ, which binds ODC and catalyzes its degradation by the 26S proteasome (Murakami et al., Biochem. Biophys. Res. Commun. 267:1-6, 2000). Again, polypeptide targets were coexpressed from plasmids with epitope tags for initial experiments, and their levels of expression were evaluated by SDS/PAGE/immunoblotting.

Of the twelve pairs of protein interactions tested by using the ODC/AZ system, five resulted in specific reductions of the target polypeptide (Table 1). For two of these five successful knock-downs, reductions of target polypeptide were entirely dependent on co-expression of AZ with the ODC chimeric fusion polypeptide, whereas, in another case, AZ enhanced the reduction caused by the ODC chimeric fusion alone. In the other two successful cases, the ODC chimeric fusion polypeptide was sufficient by itself, suggesting that fusing certain polypeptides to ODC may supplant the need for AZ. In this regard, the AZ polypeptide is known to induce a conformational change in ODC that exposes a proteasome-binding domain in its C terminus (Murakami et al., Biochem. Biophys. Res. Commun. 267:1-6, 2000), raising the possibility that some fusion partners mimic this effect of AZ.

We empirically determined that inclusion of a FL between ODC and the protein-interaction domain can be critical for successful degradation of cellular substrates, with the [Gly-Gly-Gly-Gly-Ser]₃ linker yielding best results. FIG. 19 provides an example, comparing the efficiency of a ODC fusion containing a Rb-binding fragment (amino acids 2-34) expressed with or without a FL, with respect to degradation of cellular target Rb.

Analysis of Specificity of AZ-Based Polypeptide Target Degradation. We performed a variety of experiments to explore the specificity of the ODC/AZ system for inducing target polypeptide reductions. For example, the target polypeptide TRAF6 is a member of a family of six mammalian adapter proteins with differential specificity for peptidyl motifs located in the cytosolic domains of TNF-family receptors (Ishida et al., J. Biol. Chem. 271:28745-28748, 1996). A C-terminal region in these polypeptides (C-TRAF domain) is responsible for TNFR binding. These adapter proteins also form homotrimers through the proximal portion of their TRAF domains (Arch et al., Genes Dev. 12:2821-2830, 1998). We therefore contrasted the levels of TRAF6 and TRAF2 polypeptides in cells expressing ODC chimeric fusion polypeptides containing either the TRAF domain of TRAF6 or a TRAF6-binding peptidyl motif from the cytosolic domain of RANK (“RANKp”). ODC nonfusion polypeptide served as a negative control. FIG. 20 shows the selective degradation of TRAF6 but not TRAF2 by ODC chimeric fusion polypeptides. As shown in FIG. 20, co-expressing ODC-C-TRAF6 caused reductions in the levels HA-TRAF6 but not HA-TRAF2 polypeptide. Cotransfection of AZ further decreased levels of HA-TRAF6 but not HA-TRAF2. Levels of HA-TRAF6 were reduced in cells expressing ODC-RANKp only when AZ was coexpressed. ODC-RANKp did not affect levels of HA-TRAF2, confirming the specificity of these results. ODC control polypeptide also did not alter levels of HA-TRAF6 or HA-TRAF2.

Immunoblot analysis confirmed production of the ODC-chimeric fusion polypeptides and AZ in the transfected cells. Note that accumulation of ODC-C-TRAF6 was markedly reduced, compared with ODC-RANKp, suggesting that fusing C-TRAF6 to ODC promotes its proteasome-dependent degradation independent of AZ. As expected, reductions in ODC-RANKp were induced by coexpressing AZ, consistent with AZ-dependent degradation of this ODC chimeric fusion polypeptide. Thus, we surmise that some ODC chimeric fusion polypeptides spontaneously associate with and are efficiently degraded by the 26S proteasome (e.g., ODC-C-TRAF6), whereas others (e.g., ODC-RANKp) require AZ as a cofactor for their degradation, like wild-type ODC.

AZ/ODC System Increases Rate of Target Polypeptide Degradation. Next, we undertook experiments to determine the mechanism by which target polypeptide reductions were achieved when using the ODC/AZ system. FIG. 21 shows the AZ-dependent, proteasome-dependent degradation of target polypeptide induced by ODC chimeric fusion polypeptides. First, we determined the effect of ODC chimeric fusion polypeptides on the level of mRNA encoding target polypeptides, anticipating that mRNA levels should be unchanged. Analysis of TRAF6 mRNA levels in cells transfected with plasmids encoding AZ and either ODC-C-TRAF6 or ODC-RANKp fusion polypeptides confirmed no effect on expression at the mRNA level (FIG. 20). Second, we explored the effects of pharmacological inhibitors of the 26S proteasome. FIG. 21A shows an example where HEK293T cells were cotransfected with a plasmid encoding HA-TRAF6 alone or in combination with plasmids encoding AZ and an ODC chimeric fusion polypeptide containing a TRAF6-binding peptide from the cytsolic domain of RANK (RANKp). Coexpression of ODC-RANKp and AZ with HA-TRAF6 resulted in profound reductions in the steady-state levels of HA-TRAF6 polypeptide, as determined by immunoblotting. Culturing these transfected cells with proteasome inhibitors MG132, epoximycin, or lactacystin restored HA-TRAF6 levels. In contrast, a trypsin inhibitor, used here as a control, was ineffective (FIG. 21A). These data demonstrate that ODC/AZ-induced degradation of target polypeptides is proteasome-dependent. Third, we determined the effects of the ODC/AZ system on protein half-life using ³⁵S-L-methionine pulse-chase methods. FIG. 21B shows results comparing the half-life of HA-TRAF6 in cells co-transfected with ODC-RANKp, with or without AZ. In cells expressing AZ, the half-life of HA-TRAF6 was reduced from approximately 2 h to <1 h, consistent with target polypeptide degradation occurring via an AZ-dependent mechanism. We conclude, therefore, that the ODC/AZ system induced proteasome-dependent degradation of target polypeptides without affecting mRNA expression. Pulse-chase experiments were also performed for IKK^(β), comparing cells transfected with plasmids encoding ODC versus ODC-IKK^(β). The starting levels of IKK^(β) were lower in cells expressing ODC-IKK^(β) before initiating the chase, suggesting ongoing degradation. Cold _(L)-methionine chase revealed that, indeed, the rate of degradation of IKK^(β) was faster in cells expressing ODC-IKK^(β), compared with ODC control (FIG. 21C). Fourth, we also used another approach to gauge the rates of target-polypeptide degradation where cells were transfected with ODC-expressing plasmids and then protein synthesis was shut off a day later by adding cycloheximide to cultures. Using ODC-p21 as an example, we compared the rate of degradation of the p21 target Flag-tagged Cdk2 in HEK293T cells transfected with ODC-control or ODC-p21 plasmids. Before cycloheximide treatment, steady-state levels of Flag-tagged Cdk2 were lower in the ODC-p21-expressing cells compared with ODC-control cells (FIG. 21D), suggesting ongoing degradation. After addition of cycloheximide, the rate of decline in Cdk2 polypeptide levels was faster in ODC-p21-expressing cells, as determined by densitometric quantification of immunoblot data developed by using an anti-Flag antibody with chemiluminescent detection.

Modulating Cellular Pathways by Using AZ-Based Targeted Polypeptide Degradation. Finally, we explored whether the ODC/AZ system could be used to successfully ablate the function of endogenous polypeptides. First, we examined the effects of ODC-C-TRAF6 and ODC-RANKp on induction of NFκB activity in HEK293T cells exposed to either TRAF6-dependent (e.g., IL-1) or independent (e.g., TNFα) cytokines. FIG. 22 shows the functional ablation of endogenous TRAF6 by ODC/AZ system. IL-1 induced marked increases in NFκB activity in HEK293T cells, as determined by reporter gene assays, which were reduced to near baseline levels by expression of ODC-C-TRAF6 or by coexpression of ODC-RANKp with AZ. As expected, ODC control polypeptide had no effect on NFκB induction by IL-1, confirming the specificity of these results. In contrast to the effects of ODC-C-TRAF6 and ODC-RANKp chimeric fusion polypeptides on IL-1 signaling, induction of NFκB activity by TNFα was unimpaired, consistent with the differential use of TRAF-family adapter proteins by IL-1 (e.g., TRAF6) and TNFα (e.g., TRAF2). These data thus parallel the differential effects of these ODC chimeric fusion polypeptides on TRAF6 and TRAF2 polypeptide levels (FIG. 20).

We extended these studies of effects of the ODC/AZ system on endogenous polypeptides to the tumor suppressor Rb. The Rb protein binds and suppresses E2F-family transcription factors, thus preventing them from activating target genes (Chellappan et al., Cell 65:1053-1061, 1991). FIG. 23 shows the ablation of endogenous Rb expression by using ODC/AZ system. We expressed in cells an ODC chimeric fusion polypeptide containing a Rb-binding peptide from the E7 protein, alone or in combination with AZ (FIG. 23A). Analysis of the levels of endogenous Rb protein by immunoblotting showed that the combination of ODC-E7p and AZ induced nearly complete disappearance of the Rb protein. In contrast, Rb protein levels were unaffected either by expressing ODC-E7p without AZ, or by expressing ODC control polypeptide with or without AZ (FIG. 23B). Measurements of E2F activity by using reporter gene assays demonstrated a marked increase in cells coexpressing ODC-E7p and AZ-1 (FIG. 23C), consistent with the observed loss of Rb polypeptide. We conclude, therefore, that the ODC/AZ system is capable of ablating the function of endogenous target polypeptides in cells.

Previous studies have demonstrated that ODC is degraded by the 26S proteasome through a ubiquitin-independent mechanism, whereby AZ binding induces exposure of the C terminus of ODC and accelerates its degradation by 50- to 100-fold. Normally, this pathway is induced in response to polyamines (spermine, spermidine, and putresine), which triggers AZ production, thus providing a negative feedback loop for maintaining appropriate intracellular levels of these molecules (reviewed in Coffino, Nat. Rev. Mol. Cell Biol. 2:188-194, 2001). We exploited the ODC/AZ system for targeting degradation of selected polypeptides in cells. The ODC/AZ system affords the advantage over most ubiquitin-pathway-based strategies that posttranslational modification of the target polypeptide (by ubiquitination) is not required, thus providing a more direct means of delivering ligand/target complexes to the proteasome for degradation. Indeed, compared with a variety of ubiquitin-pathway-based approaches examined, we found the ODC/AZ system to be more effective at achieving degradation of a test set of twelve target polypeptides for which interacting polypeptides are known. Successful degradation was achieved in five of twelve test cases, suggesting that some polypeptides are recalcitrant to this targeting approach. Multiple explanations could account for the intractability of certain polypeptide targets, including (i) insufficient affinity interactions of the protein ligands with their cellular target polypeptides; (ii) dissociation of ligand and target during digestion of the ODC-ligand fusion by the proteasome, thus stripping the target polypeptide off; and (iii) impeded entry of the target polypeptide into the pore of the proteasome because of rigid protein structure, necessitating protein unfolding. Thus, the tractability of specific polypeptide targets to degradation by the ODC/AZ system must be empirically determined.

A potential concern with the ODC/AZ system is that expression of ODC-fusion polypeptides or AZ in cells may alter polyamine levels, leading to artifactual changes in cell growth, chromatin structure, or other cellular events. Measurement of cell-division rates for HeLa and HEK293T cells used for our experiments revealed no apparent effect of ODC-fusion polypeptides or AZ, suggesting that at least some types of cells are not particularly sensitive to these manipulations. However, more subtle changes in cells overexpressing ODC fusion polypeptides and AZ conceivably may occur and therefore should be considered in interpreting data derived from use of the ODC/AZ-based approach to targeted protein degradation. The suitability of this approach may also be dependent on the endogenous levels of AZ and AZ inhibitors in particular types of primary cells or cell lines.

This basic system can be improved in a number of ways. For instance, mutant versions of ODC that lack enzymatic activity but which preserve proteasome-dependent degradation obviate untoward effects on polyamine synthesis, particularly non-dimerizing mutants which cannot bind endogenous ODC. Similarly, production of complementary pairs of ODC and AZ mutants that bind each other but fail to interact with their endogenous (wild-type) counterparts provide a means to avoid effects on polyamine synthesis. It should be noted, however, that AZ may have additional cellular targets besides ODC, a possibility that must be considered, including cyclin D1 and Smad1, at least in certain type of cells (Newman et al., J. Biol. Chem. 279:41504-41511, 2004; Lin et al., BMC Cell Biol. 3:15, 2002). One possible advantage of the ability of polyamines to induce AZ expression is that it might be possible to forego transfection of AZ-encoding plasmid by adding polyamines or polyamine analogues to the cell cultures.

Results obtained with the ODC/AZ system and other previously reported approaches for inducing proteasome-dependent degradation of specific proteins (Stack et al., Nat. Biotechnol. 18:1298-1302, 2000; Lindsten et al., Nat. Biotechnol. 21:897-902, 2003; Zhou et al., Mol. Cell 6:751-756, 2000; Liu et al., Biochem. Biophys. Res. Commun. 313:1023-1029, 2004; Sakamoto et al., Proc. Natl. Acad. Sci. USA 98:8554-8559, 2001; Su et al., Proc. Natl. Acad. Sci. USA 100:12729-12734, 2003) should be interpreted with understanding that the particular protein ligand that is chosen may have multiple cellular targets, including unknown or unanticipated protein targets in addition to known interacting proteins intended for targeted degradation. Thus, phenotypes created by these targeted polypeptide-degradation methods could potentially reflect the loss of expression of several interacting polypeptides. When searching for functions of gene products where more specific methods such as antisense or small interfering RNA have failed to yield phenotypes, ablating the expression of the interrogated gene product's interacting partners may provide clues for eventually understanding its function. Moreover, targeted protein-degradation methods that attack interacting proteins afford an approach for dealing with multigene families, where a particular protein ligand may interact with multiple members of a family of homologous gene products, thereby ablating expression simultaneously of several redundant members and revealing phenotypes that would be undetected by nucleic-acid-based methods for silencing gene expression at the mRNA.

While the invention has been described in detail with reference to certain preferred embodiments thereof, it will be understood that modifications and variations are within the spirit and scope of that which is described and claimed.

Summary of Sequences

SEQ ID NO:1 is a cDNA (and the deduced amino acid sequence) encoding a Siah 1α of the present invention.

SEQ ID NO:2 is the deduced amino acid sequence of a Siah 1α protein of the present invention encoded by SEQ ID NO:1.

SEQ ID NO:3 is a cDNA (and the deduced amino acid sequence) encoding a human SIP-L polypeptide of the present invention.

SEQ ID NO:4 is the deduced amino acid sequence of a human SIP-L protein of the present invention encoded by SEQ ID NO:3.

SEQ ID NO:5 is a cDNA (and the deduced amino acid sequence) encoding a human SIP-S polypeptide of the present invention.

SEQ ID NO:6 is the deduced amino acid sequence of a human SIP-S protein of the present invention encoded by SEQ ID NO:5.

SEQ ID NO:7 is a cDNA (and the deduced amino acid sequence) encoding a human SAF-1α polypeptide of the present invention.

SEQ ID NO:8 is the deduced amino acid sequence of a SAF-1α protein of the present invention encoded by SEQ ID NO:7.

SEQ ID NO:9 is a cDNA (and the deduced amino acid sequence) encoding a human SAF-1β polypeptide of the present invention.

SEQ ID NO:10 is the deduced amino acid sequence of a SAF-1β protein encoded by SEQ ID NO:9.

SEQ ID NO:11 is a cDNA (and the deduced amino acid sequence) encoding a human SAF-2 polypeptide of the present invention.

SEQ ID NO:12 is the deduced amino acid sequence of a SAF-2 protein encoded by SEQ ID NO:11.

SEQ ID NO:13 is a cDNA (and the deduced amino acid sequence) encoding a human SAD polypeptide of the present invention.

SEQ ID NO:14 is the deduced amino acid sequence of a SAD protein encoded by SEQ ID NO:13.

SEQ ID NO:50 is the amino acid sequence of the ODC-fusion protein. 

1. An isolated polynucleotide that comprises a promoter sequence operably linked to a sequence that encodes a chimeric protein that comprises a target-protein binding domain operatively linked to a protein-degradation binding domain of ornithine decarboxylase, wherein binding of the target-protein binding domain of the chimeric protein to a target protein in a cell induces degradation of the target protein in the cell.
 2. The isolated polynucleotide of claim 1 wherein the protein-degradation binding domain of ornithine decarboxylase is an ornithine decarboxylase C-terminal region polypeptide.
 3. The isolated polynucleotide of claim 1 wherein the protein-degradation binding domain of ornithine decarboxylase is a human ornithine decarboxylase C-terminal region polypeptide.
 4. The isolated polynucleotide of claim 3 wherein the ornithine decarboxylase C-terminal region polypeptide is a full-length human ornithine decarboxylase C-terminal region polypeptide.
 5. The isolated polynucleotide of claim 1 wherein the chimeric protein further comprises a linker sequence between the target-protein binding domain and the protein-degradation binding domain of ornithine decarboxylase.
 6. The isolated polynucleotide of claim 5 wherein the linker sequence is a flexible linker sequence.
 7. The isolated polynucleotide of claim 6 wherein the flexible linker sequence is selected from the group consisting of residues 31 to 94 of a Bcl-2 protein, a Gly-Gly-Pro tripeptide, and [Gly-Gly-Gly-Gly-Ser]₃ (SEQ ID NO: 61).
 8. The isolated polynucleotide of claim 7 wherein the flexible linker sequence is [Gly-Gly-Gly-Gly-Ser]₃ (SEQ ID NO: 61).
 9. The isolated polynucleotide of claim 1 wherein the chimeric protein comprises, in order from N-terminus to C-terminus, (a) a target-protein binding domain, (b) a flexible linker sequence, and (b) a protein-degradation binding domain of ornithine decarboxylase.
 10. The isolated polynucleotide of claim 9 wherein the protein-degradation binding domain of ornithine decarboxylase comprises an ornithine decarboxylase C-terminal region.
 11. The isolated polynucleotide of claim 1 wherein the chimeric protein further comprises an epitope tag sequence.
 12. A pharmaceutical composition comprising a polynucleotide of claim 1 and a pharmaceutically acceptable carrier.
 13. The pharmaceutical composition of claim 12 further comprising a polyamine.
 14. The polynucleotide of claim 1 further comprising a second promoter sequence operably linked to a sequence that encodes an antizyme protein.
 15. The polynucleotide of claim 14 wherein the antizyme protein is a human antizyme protein.
 16. The polynucleotide of claim 14 wherein the antizyme protein is a full-length antizyme protein.
 17. A pharmaceutical composition comprising a polynucleotide of claim 14 and a pharmaceutically acceptable carrier.
 18. A cell comprising an isolated polynucleotide of claim
 1. 19. A mammal comprising the cell of claim
 18. 20. A mouse comprising the cell of claim
 18. 21. A kit comprising: (a) a composition comprising an isolated polynucleotide that comprises a promoter sequence operably linked to a sequence that encodes a chimeric protein that comprises a target-protein binding domain operatively linked to a protein-degradation binding domain of ornithine decarboxylase, wherein binding of the target-protein binding domain of the chimeric protein to a target protein in a cell induces degradation of the target protein in the cell; and (b) a composition comprising an isolated polynucleotide that comprises a promoter sequence operably linked to a sequence that encodes an antizyme protein; and (c) instructions for use.
 22. An isolated chimeric protein that comprises a target-protein binding domain operatively linked to a protein-degradation binding domain of ornithine decarboxylase, wherein binding of the target-protein binding domain of the chimeric protein to a target protein in a cell induces degradation of the target protein in the cell.
 23. The isolated chimeric protein of claim 22 wherein the protein-degradation binding domain of ornithine decarboxylase is an ornithine decarboxylase C-terminal region polypeptide.
 24. The isolated chimeric protein of claim 22 comprising a full-length mature human ornithine decarboxylase C-terminal region polypeptide.
 25. The isolated chimeric protein of claim 22 comprising a protein-degradation binding domain of human ornithine decarboxylase.
 26. The isolated chimeric protein of claim 22 further comprising a linker sequence between the target-protein binding domain and the protein-degradation binding domain of ornithine decarboxylase.
 27. The isolated chimeric protein of claim 26 wherein the linker sequence is a flexible linker sequence.
 28. The isolated chimeric protein of claim 26 wherein the linker sequence is selected from the group consisting of residues 31 to 94 of a Bcl-2 protein, a Gly-Gly-Pro tripeptide, and [Gly-Gly-Gly-Gly-Ser]₃ (SEQ ID NO: 61).
 29. The isolated chimeric protein of claim 28 wherein the linker sequence is [Gly-Gly-Gly-Gly-Ser]₃ (SEQ ID NO: 61).
 30. The isolated chimeric protein of claim 22 comprising, in order from N-terminus to C-terminus, (a) a target-protein binding domain, (b) a flexible linker sequence, and (b) a protein-degradation binding domain of ornithine decarboxylase.
 31. The isolated chimeric protein of claim 22 further comprising an epitope tag sequence.
 32. A pharmaceutical composition comprising the chimeric protein of claim 22 and a pharmaceutically acceptable carrier.
 33. The pharmaceutical composition of claim 32 further comprising a polyamine.
 34. A method of degrading a target protein in a cell comprising providing in the cell an isolated chimeric protein that comprises a target-protein binding domain operatively linked to a protein-degradation binding domain of ornithine decarboxylase, wherein binding of the target-protein binding domain of the chimeric protein to a target protein in the cell induces degradation of the target protein.
 35. The method of claim 34 comprising providing in the cell the isolated chimeric polypeptide by expressing in the cell a polynucleotide that comprises a promoter sequence operably linked to a sequence that encodes the chimeric protein.
 36. The method of claim 34 comprising providing in the cell the isolated chimeric protein and an antizyme protein by expressing in the cell (a) a first polynucleotide that comprises a first promoter sequence operably linked to a sequence that encodes the chimeric protein, and (b) a second polynucleotide that comprises a second promoter sequence operably linked to a sequence that encodes the antizyme protein.
 37. The method of claim 34 comprising providing in the cell the isolated chimeric protein and an antizyme protein by expressing in the cell a polynucleotide that comprises a first promoter sequence operably linked to a sequence that encodes the chimeric protein and a second promoter sequence operably linked to a sequence that encodes the antizyme protein.
 38. The method of claim 34 further comprising contacting the cell with a composition comprising a polyamine.
 39. The method of claim 38 wherein the composition comprising the polyamine comprises one or more members selected from the group consisting of spermine, spermidine, putrescine, and analogs thereof.
 40. A method of identifying a phenotype of a target protein in a cell comprising (a) providing in the cell an isolated chimeric protein that comprises a target-protein binding domain operatively linked to a protein-degradation binding domain of ornithine decarboxylase, wherein binding of the target-protein binding domain of the chimeric protein to the target protein in the cell induces degradation of the target protein, and (b) observing a change of phenotype of the cell.
 41. A method of treating a patient having a disease characterized by expression of a target protein in a cell of the patient, the method comprising providing in the cell an isolated chimeric protein that comprises a target-protein binding domain operatively linked to a protein-degradation binding domain of ornithine decarboxylase, wherein binding of the target-protein binding domain of the chimeric protein to the target protein in the cell induces degradation of the target protein.
 42. A method of identifying a polynucleotide that encodes a target-protein binding domain that binds a target protein comprising: (a) expressing in the cell a vector that comprises a promoter sequence operably linked to a protein-coding sequence that comprises (i) a test polynucleotide sequence, and (ii) a polynucleotide sequence that encodes a protein-degradation binding domain of ornithine decarboxylase, and (b) observing a change of phenotype of the cell, wherein the change of phenotype indicates that the test polynucleotide sequence encodes the target-protein binding domain and that binding of the target-protein binding domain to the target protein in the cell induces degradation of the target protein. 